Genetic Diversity in a Collection

[PhoenixGate]

I have a couple of questions. The
first is, how do you as keepers typically maintain genetic diversity
in your collection of snakes (assuming that you breed them) or do you
pay attention to it at all? I know inbreeding happens in order to
prove out a new morph, for example breeding an unusual looking baby
back to its parent. Now, if your maintaining a small colony and
holding back a few babies as future breeders in an effort to save
money on new breeders, or if the baby has a gene that's expensive to
acquire by buying a new snake, at some point a lot of the snakes in
your collection will be related to each other. How does this impact
the snakes, or is there any measurable difference in the health of
closely related captive snakes vs their wild brothers and sisters?


My second question is this; I have seen
people on this site mention receiving papers with a newly purchased
snake. What do these papers consist of, a pedigree as well as a
feeding chart? How do you guys keep track of the lineage of the
snakes you breed and sell? Or do you keep track of this at all?

[Pythonfriend]

inbreeding should be avoided, except in the cases when its required.

as few inbreeding as possible, as much inbreeding as neccessary.

avoid inbreeding whenever possible. but there often are reasons to do it. to hit a super project or a recessive or double recessive project, it often cannot be avoided.

reptiles appear to be more resilient when it comes to inbreeding, compared to mammals. but that is no sure bet.

[CryHavoc17]

Most people seem to try pretty hard to outcross regularly within their own collection for genetic diversity. However, the idea that the overall gene pool within the hobby hasn't been inbred to a massive extent is pretty ridiculous.

Example a)
Joe proves out a new mutation. Keeps all the babies and breeds them together to see if there is a super. There is. He sells the non supers of those inbreedings to Mike, who wants in on the project, then makes sure to keep track of genetic diversity going forward. Mike loves the super and want some himself. So he inbreeds the minimal amount to get him some supers, and makes sure to outcross after that. Mike sells to Charlie, charlie sells to Judy, Judy sells to Chris and on an on it goes.

Everybody is only inbreeding as little as possible, but every time someone new comes into the project more inbreeding takes place. So ten or 15 years later the line has been inbred over and over and over again, even though everyone in the project is trying to avoid it. If you buy from chris who bought from judy who bought from charlie who bought from joe your animal has been inbred a LOT.

Example b) joe proves out a new mutation with a super. Doesnt give a crap about inbreeding and just wants to make as much money as possible. So he just keeps crossing sibs together, or offspring back to parents. 10 or 15 years down the line, if you buy from joe, it is a guarantee your babys line has been inbred over and over and over again

Example A is considered doing the right thing, example B is considered unethical. Wait, really? Whats the difference?

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[Pythonfriend]

Cryhavoc, its not as bad as you make it sound.

if you take a really inbred super enchi and breed it to a really inbred super fire, as long as the super enchi has different ancestors than the super fire, the offspring will not be inbred.

there are calculators that can be used to calculate an inbreeding coefficient for an individual based on all available knowledge about the ancestry. and with the right pairing, its possible to reset it back to zero.

if you go far enough back in time, every individual is related to every other individual. its even true for humans. for example, more than 30 million US citizen are related to the 102 pilgrims that arrived on the mayflower, and the majority of chinese people have Gengis Khan in their ancestry. also, most people of european descent have the ability to digest lactose, people of other origin can digest lactose as children but lose that ability in adulthood. this traces back to a single mutation that happened in a single person around 6000 years ago somewhere in central europe. so if you can tolerate fresh milk, congratulations, we are related. in iceland there is a popular smartphone app, if you enter two icelandic people, it performs a database search based on records that go back centuries, and in most cases it will find the name of the last common ancestor.

[Darkbird]

Now, I'm just going by something I heard, I think it was on here, but I can't back it up. Bps in the wild aren't all that genetically diverse to begin with. Since they don't tend to travel long distances, I think it could be said that the specimens in a given area are going to be related anyway. So it would seem that they may have a naturally occurring tolerance to inbreeding that would be lacking in more "traveled" animals. Not that I'm looking to inbreed the hack out of mine or anything, it just seems a logical explanation for why we can get away with so much of it when it very quickly has bad effects in other animals.

[satomi325]

Got to look at the natural history of the species.
Inbreeding in reptiles is really common, even out in nature. They are a non migratory species that stay local so outcrossing to a new population is pretty rare. They couldn't tell if they were breeding a relative or not. Its safe to say that breeding with relatives is not uncommon. That's why you get special locality or specific line trait based animals of the same species. It just makes them have a higher homozygosity.

Natural selection keeps the population strong and selects against weakness/negative traits. In captivity, the humans are the ones responsible for that selection.


Inbreeding or line breeding is fine to do as long as the snakes are healthy and you don't think they carry any heritable disability. Many often prove out recessive genetics that way.
Reptiles do not have the same issues that mammals have when inbreeding or line breeding. (Not counting the morphs that are prone to genetic defects)


So with that said, if you choose to inbreed or line breed, I personally wouldn't go overboard with it and only choose to do a few generations at the very most. Breeding healthy animals should be more important than genetic potential. Although keeping low genetic diversity can also prevent you from bringing in animals with negative traits into your lines.

There are pros and cons to both outcrossing and inbreeding. Got to breed smart.

For example, I keep my rodent colony very homogeneous. I do it because I know my rats are genetically sound with no heritable illnesses. I don't want to bring in new genetics that can introduce flaws and hinder my lines.

[OctagonGecko729]

I'd add to what Satomi was saying. There is no problem with "inbreeding" itself. All inbreeding does is increase the chance of specific genes to be turned on. Theres nothing wrong with this so long as the genes that are being turned on are healthy. The problem with mammalian inbreeding is that a lot of mammals have a ton of bad genes in their genome. You don't run into many bad genes in reptiles or insects. There are also plenty of mammals such as rodents which have little problems when they are inbred. The fact that human inbreeding even for one generation generally causes significant health concerns is a testament to how many flawed genes we still have in our genome. Many of these other types of organisms have been around far longer then mammals and have had much more time to weed out the bad genes through natural selection.

[bcr229]

If it's a big enough concern after a few generations most breeders could simply sell or trade off their foundation stock. For instance, if I have one mohave sire and he's both daddy and granddaddy to every mohave or mohave combo in my collection, I could trade him for a different mohave male, or buy a mohave combo male to use with my girls if I wanted to try for supers, etc.

[OhhWatALoser]

I see no reason to treat an inbred pairing any different. If issues become common, stop breeding that pair, whether they be brother and sister or 50 generations removed. If there are no issues, why the heck wouldn't you keep going? Genetic diversity is good for adapting if the status quo changes, such as a disease or environmental change. Line breeding is the way to go for a strong animal, assuming you get the right parts together.

Humans find ways to cope with the negative traits and survive, just about every other species just lets that animal die, so our gene pool filled with negative genes that should of took out some of our lines out a long long time ago. Damn developed brain screwing up our gene pool.

[Krynn]

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. Most 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. 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).

Lets pretend we are looking at a wild population, and a developing snake acquires a dominant mutation that causes kinking. Chances are that the snake will die very early on in its life. In the rare chance that the snake manages to survive and reproduce, 100% of its offspring will have kinking and also likely die. Natural selection quickly eliminates the dominant kinking gene from the population. You can imagine the same scenario where the snake instead has a co-dominant mutation, and the heterozygous form has mild kinking. The snake might survive and reproduce, but 50% of the offspring are mildly kinked. In the event that two kinked snakes mate, 25% of the offspring are the completely unviable super form. Before long, the co-dominant kinked snakes are outcompeted by the normal unkinked snakes and the gene is still removed from the population.

Now imagine the snake is born with with a recessive kinked gene. The snake is born completely healthy, and has 50% het kinked offspring that are also completely healthy. Every so often, a het kinked snake will mate with another het kinked snake and produce kinked young. For this reason, normal snakes still slightly out-compete kinked snakes, but often not enough to remove it from the population because it can always hide in the het form. Lots of disadvantageous recessive alleles occur at low frequencies in all populations, including us. Although the chance of having any particular mutation is incredibly low, the chance of having ANY such mutation is actually quite high. When mating with an unrelated individual, the chances that you are both het for the same mutation is incredibly low. The problem with inbreeding is that you share a proportion of your genes with your relatives, and the chance that you will express disadvantageous genes is much higher.


How bad is inbreeding?

So inbreeding is bad because it increases the chance that you express rare, disadvantageous, recessive alleles. However, as mentioned already in this post, most animals inbreed at least some of the time and are somewhat resilient to low levels of inbreeding. For the most part, inbreeding problems manifest themselves when you have many generations of inbreeding without introducing new genes from unrelated individuals. The likelihood of producing offspring that suffer from inbreeding depression comes down to what proportion of genes you share with your mate. Everyone shares 50% with their parents and siblings, 25% with their half siblings, 12.5% with cousins etc. By the time you get down to someone who is your third cousin you actually only less then 1% of your DNA with them.

So although I am certainly not advocating having children with your cousins, having inbreeding events every once and a while is not necessarily a bad thing (genetically speaking).

As far as snakes are concerned, inbreeding can be a problem when you are inbreeding snakes that are inbred to begin with. Inbreeding causes offspring to be more genetically related then you would expect (from the percentages above). If you bred half siblings together, normally they would share 25% of their genes, but in an inbred strain they may share 35-40% of their genes instead. Paired full-sibs that are inbred may share 75-80% of their genes.

I dont want to read all this. Just answer my question. Is it ok to inbreed my snakes?

This post is basically a long and comprehensive way of saying what several people have already said in this post. A little bit of inbreeding isn't all that bad. After all it is the only way that a breeder can start producing the recessive mutations that we all love. With that being said, its always good to throw in some genetic variation whenever you can (even if its a third or fourth cousin). When starting a breeding project from scratch, perhaps try to get your snakes from several different breeders rather then all from the same clutch. This will give you some opportunities to inbreed for a generation or two down the line with less risk.

Remember, the reason that sexual reproduction evolved was not so that animals could enjoy the orgasm. It was to promote genetic diversity. Let us all try to keep captive snake populations as diverse as possible, so we can avoid inbreeding depression now and in the future.

Cheers,
-Krynn