Genetic Diversity in a Collection

[T&C Exotics]

Krynn I completely disagree with you on this in relation to reptiles. More specifically ball pythons. They have extremely small ranges in the wild and do not just go for a walk to get away from their family. As newly hatched baby they go to the closest safe spot and shed and then to to the closest spot to eat and drink odds are that in Africa there are not many places like that and that the babies will generally go to the same spots. Yes over time they will move on to some extent but not a whole lot. Why do you think any recessive mutation has been found in the wild more than once? It is because 2 snakes carrying the same mutant genes mated and produced them. That would indicate that animals very closely related breed a lot in reptiles.

knowledge is earned not learned

[Krynn]

Krynn I completely disagree with you on this in relation to reptiles. More specifically ball pythons. They have extremely small ranges in the wild and do not just go for a walk to get away from their family. As newly hatched baby they go to the closest safe spot and shed and then to to the closest spot to eat and drink odds are that in Africa there are not many places like that and that the babies will generally go to the same spots. Yes over time they will move on to some extent but not a whole lot. Why do you think any recessive mutation has been found in the wild more than once? It is because 2 snakes carrying the same mutant genes mated and produced them. That would indicate that animals very closely related breed a lot in reptiles.

knowledge is earned not learned

Hi T & C,

I am very curious how you could know this. There is very little research done on ball pythons in the wild, and nothing is known about male dispersal or kin discrimination (that I know of). If you have any sources about dispersal, I would love for you to PM them to me . In the inbreeding depression literature, there has been alot less work done in amphibians and reptiles in comparison to mammals and birds. You would be surprised at how some individuals will travel even in seemingly stationary animals.

Yes we do get a fair amount of recessive mutations from the wild, but this is not support for the idea that wild ball pythons are inbred. Recessive mutations are rare, but present in all sorts of animal populations. This even happens even in species that we know to have methods of inbreeding avoidance. Just two summers ago, I found an albino deer mouse in a wild population that we know is not particularly inbred.

Cheers,
-Krynn

[Pythonfriend]

if one in 1000 animals are carriers for a recessive gene, even without inbreeding, one in a million will be a visible recessive. the natural population is gigantic, so it would show up every now and then. so thats no evidence for anything. then there are big breeding farms in africa, which have a more limited gene pool.

its just a guess, but i would not be surprised at all if males in the wild start fighting as soon as they reach sexual maturity, or maybe the adult male will drive them away.

i do believe reptiles to be somewhat more resilient when it comes to inbreeding. that doesnt mean that there wont be any negative consequences at all. 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. 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.

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.

most big breeders seem to care about the issue and say that they are taking active steps to minimize inbreeding. fortunately, the larger the collection is, the easier it gets to avoid inbreeding. as the collection size goes up, the amount of possible pairing grows exponentially, and much faster than the amount of pairings that would lead to inbreeding. with a large enough collection, its even possible to do a double recessive project without inbreeding.

Bill Brant from Gourmetrhodent has a gigantic collection, and he has a computer system in place that calculates the inbreeding coefficient for every animal in the collection, and for each hatchling he gets a number that tells him how strongly the genetics of the hatchling are already represented in the collection. basically the system calculates how closely related the hatchling is to every other snake in the collection. and he uses it to inform his decisions on what to hold back. so, some breeders REALLY invest A LOT of effort and brainpower to make sure inbreeding is under control.

[OctagonGecko729]

I gotta disagree with the "sexual reproduction is to promote genetic diversity".

The way you stated it made me interpret that to be that sexual reproduction arose "in order to do ____". This couldn't be more incorrect and goes against everything we know about natural selection leading to "evolution".

No, sexual reproduction was merely a set of random mutations which proved to be advantageous for those organisms. There isn't a "goal" when it comes to evolution. There is simply a whole lot of random variables that either live and reproduce or die. Sexual reproduction does offer another division which increases genetic diversity within the developing embryo but this really doesn't matter in regards to inbreeding. When sexual reproduction was "selected" for the methodology of reproduction, it simply offers more variables. It doesn't make those variables better then mitotic divisions it only casts the genetic net wider.

If we artificially made a pair of organisms that were perfect but exactly the same. You could inbreed them indefinitely without issue.

Again, the problem with mammals inbreeding is that we diverged very recently in the grand scheme of life on this planet. Insects, reptiles, and micro organisms have been here far longer and have had much more time to get rid of defects. Yes inbreeding can be deleterious for an organism but it can also be beneficial. The exact same is true of very out crossed animals. Either the bad genes align up or they don't.

[Pythonfriend]

well, the benefit of having two copies of the genome is that one gene is broken, you are not dead. the other one simply takes over. this mechanism provides resilience against genetic defects. inbreeding undermines this mechanism.


and the benefit of sexual reproduction is the recombination of genes. if one individual has one beneficial mutation, and a different individual has a different beneficial mutation, sexual reproduction makes it possible that in the end, all have both beneficial mutations. without sexual reproduction, one part of the species has one of the beneficial mutation, and the rest has the other one, and the only way to improve is to wait for another beneficial mutation to come along. so it greatly speeds up the process of evolution. again, inbreeding undermines the mechanism, one gene needs to be able to float around in the entire gene pool of the population. if you have a bunch of inbred families and not much cross-breeding going on, the process is slowed down and the benefit of sexual reproduction is diminished.

you never get a perfectly clean genome, defects get introduced by radiation, by carcinogens, and by retroviruses. the diploid set of chromosomes and sexual production both help adress this issue, inbreeding makes it worse.

but then, in captivity it has been done with lab rats, there are lines that have been inbred for hundreds of generations over many decades in the most extreme way: brother to sister in every single generation. it has no benefit for the rats, and early in the process there are a lot of deformities and health issues. the benefit is that after a few hundred generations, they are basically all genetically identical, which helps in scientific research. real drawbacks are that one infection can eliminate the whole colony, and they all have the same weaknesses. in one line, they all tend to be overweight, they all tend to get diabetes, they all drink alcohol the first time you offer it to them, and they all have the same behavioral quirks. personally i think thats quite messed up. in an evolutionary sense, they stopped evolving, they are like frozen in time. but hey, no need to sequence, you can just download their genome online.

[PhoenixGate]

I've read up quite
a bit about inbreeding in captivity and the wild, so I hope I can add
to this conversation. Feel free to criticize:

I
think the suggestion that reptiles can tolerate more inbreeding than
mammals is slightly misleading. // 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. Ball pythons are NOT cheetahs. Genetically they will
respond to inbreeding differently. The mere fact that many of the
big name breeders have had little trouble producing healthy snakes,
especially snakes with genes that derived from just one or two
imported animals, is telling.// wild animals
inbreed to a small degree without consequence, and almost all animals
have some sort of method for avoiding inbreeding because of the
negative consequences. Most inbreeding avoidance strategies include
kin recognition (being able to tell who your relatives are), and male
dispersal. There are of course a few exceptions to this rule (naked
mole rats, ants and bees are the best examples of this), but I see no
reason to believe that inbreeding does not effect reptiles in the
same way as mammals.

Why is inbreeding bad?

As
you all know, animal populations accumulate mutations. Some
of these mutations are advantageous to the animal, but most of them
are disadvantageous
and decrease the survival of an animal. //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. Also, a negative mutation
may not be so negative. For example, humans carry a gene that is
broken (non-functional) that has to due with muscle development. In
other apes this gene produces the awe-inspring strength gorillas and
chimpanzees have. From a purely evolutionary perspective, this is a
negative mutation, creating humans that are much weaker than their
gorilla or chimpanzee cousins. However this mutation may have put
less pressure on muscle attachment sites to human skulls, allowing
our braincases to expand. So, what appears to be a negative mutation
is in actuality a positive one.// Many genetic
traits work the exact same way as the color and pattern morphs that
we all love. There are dominant traits, co-dominant traits, and
recessive traits. I will give an example of how inbreeding causes
problems, using kinking as an example of a disadvantageous trait.
(Disclaimer: Im not entirely sure that kinking is caused by
inbreeding, but I think it is an entirely possible explanation at
least in some lines. Feel free to substitute kinking in this example
with any other disadvantageous trait you can think of).

[PhoenixGate]

I gotta disagree with the "sexual reproduction is to promote genetic diversity".

The way you stated it made me interpret that to be that sexual reproduction arose "in order to do ____". This couldn't be more incorrect and goes against everything we know about natural selection leading to "evolution".

No, sexual reproduction was merely a set of random mutations which proved to be advantageous for those organisms. There isn't a "goal" when it comes to evolution. There is simply a whole lot of random variables that either live and reproduce or die. Sexual reproduction does offer another division which increases genetic diversity within the developing embryo but this really doesn't matter in regards to inbreeding. When sexual reproduction was "selected" for the methodology of reproduction, it simply offers more variables. It doesn't make those variables better then mitotic divisions it only casts the genetic net wider.

If we artificially made a pair of organisms that were perfect but exactly the same. You could inbreed them indefinitely without issue.

Again, the problem with mammals inbreeding is that we diverged very recently in the grand scheme of life on this planet. Insects, reptiles, and micro organisms have been here far longer and have had much more time to get rid of defects. Yes inbreeding can be deleterious for an organism but it can also be beneficial. The exact same is true of very out crossed animals. Either the bad genes align up or they don't.

Actually yes, the entire purpose of sexual reproduction is to randomize the genes. When meiosis occurs the organism isn't just splitting the chromosomes in the sex sell, it's randomizing the sequences of the genes as well. This is where a
lot of the genetic mutations happen. On average, each human has about 60 genetic mutations. The entire point of this is to create genetic diversity in the species, or novelty, so that species will have the chance to survive. Natural selection absolutely cannot happen without novelty.

[PhoenixGate]

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?

[OhhWatALoser]

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.

[Krynn]

I gotta disagree with the "sexual reproduction is to promote genetic diversity".

The way you stated it made me interpret that to be that sexual reproduction arose "in order to do ____". This couldn't be more incorrect and goes against everything we know about natural selection leading to "evolution".

No, sexual reproduction was merely a set of random mutations which proved to be advantageous for those organisms. There isn't a "goal" when it comes to evolution. There is simply a whole lot of random variables that either live and reproduce or die. Sexual reproduction does offer another division which increases genetic diversity within the developing embryo but this really doesn't matter in regards to inbreeding.

Completely agree 100% on the wording. Traits dont evolve for a purpose. I disagree on the point that sexual reproduction doesnt matter in regards to inbreeding. Perhaps I dont understand what you are trying to say, but the problem of inbreeding depression is tightly linked with sexual reproduction.

If we artificially made a pair of organisms that were perfect but exactly the same. You could inbreed them indefinitely without issue.

Again, the problem with mammals inbreeding is that we diverged very recently in the grand scheme of life on this planet. Insects, reptiles, and micro organisms have been here far longer and have had much more time to get rid of defects. Yes inbreeding can be deleterious for an organism but it can also be beneficial. The exact same is true of very out crossed animals. Either the bad genes align up or they don't.

If you just go into google scholar and type "inbreeding depression in reptiles" im sure you would find otherwise. Inbreeding depression is almost universal across the animal kingdom with only few exceptions (and they are not taxanomic exceptions). The only group that I would agree with you about is micro-organisms.