# Inbreeding



## narhay

It is so prevalent in this hobby that it is almost sickening. I understand that it is sometimes hard to get more than one source of fish, but we are compromising the genetic diversity for aquarium raised fish.

I for one am trying to trade fish for fish, diversifying my genetic pool. It is difficult with uncommon fish, but I am trying. Too often do I hear of people buying a group of 6 F1 fish, letting them pair off and then selling the fry touted as F2 (signifying quality for some, but for me all I see is inbred stock).

Anyone else think that this is possibly the greatest silent threat to aquarium strains? Who knows if the wild stock will ever get cut off due to anthropogenic causes?


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## why_spyder

Inbreeding isn't a bad thing - if done responsibly. F1 X F1 is far from being bad. Have you done some searching around on this forum for topics regarding inbreeding? If not, I would seriously look around - there is some great information regarding this topic on here.


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## Number6

I would seriously urge you to look into inbreeding depression and outbreeding depression.

The inbreeding bogeyman is slowly dying off (thank the stars) as we find fish like Kribs that preferentially inbreed in the wild, etc.

Inbreeding should be viewed solely as a tool for trait reinforcement and outcrossing should be viewed solely as a trait obtaining move.... it is a balance appropriate to the species that is important. For mbuna, the degree of inbreeding that works best is far higher than the often hyrbidized shell dwellers or sand sifters of lake Tanganyika.

Now here's the kicker... random inbreeding or outcrossing will wreck your broodstock pretty quickly IME. So what works? Big pools of potential mates and letting the fish pick their own mates. Amazingly, they seem to be smarter at this than we are.

When allowed to pick their own mates, deformities or other issues drop dramatically or disappear altogether.

Funny... it's almost like they have an instinct for it or something... :thumb:


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## narhay

I also agree with allowing the fish to pick their mates from large pools of stock. I am not against this. What I am against is how prevalent inbreeding is, especially down the line. Most hobbyists do not outcross.

Inbreeding increases the ratio of homozygotes. This includes recessive disease alleles. When these alleles increase in proportion to the population, they will probably not fix to 0.

All I am saying is that our brood stock is going to be compromised many many years from now if there is not new genetic inflow.

Ok, so there is the cheetah example...lower fitness due to outcrossing.


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## Number6

narhay said:


> Ok, so there is the cheetah example...lower fitness due to outcrossing.


 My favorite example of our arrogance towards life. 
Captive breeding programs concerned themselves with the same assumptions you make and so tried to maximize diversity in the captive pairings. Every cheetah was used and as much outcrossing to wild as possible was attempted.

Fitness, fertility, etc. dropped DRAMATICALLY. Sceintists isntantly predicted the extinction of cheetahs until a study was done on the wild ones... seems they were fine.

Odd... why were the wild ones fine?

What you don't realize is that homozygosity without the presence of deleterious alleles is a non-issue... outcrossing in the presence of deleterious alleles is similarly a disaster. As your deleterious allele now increases in frequency it becomes harder and harder to find individuals that aren't carriers. It also does NOT take 2 copies of a bad gene for it to be expressed.

So is inbreeding the bogeyman? or is it the deleterious alleles?

answer is obvious...

Proper culling while breeding tight (within somewhat related bloodlines) is all that is needed. This is born out time and time again in natural populations of animals. 
Even in my own lifetime, I can see it in action. I added a small number of pumpkin seed sunfish and large mouth bass to a pond located on my parent's property. This pond has been inbreeding merrily for 25 plus years.

You can pull out perfect sunfish after perfect sunfish and you will never find any deformed, strange looking, or anything.

This experience is not matched at other lakes where there are other sunfish species alongside the pumpkin seeds. I wonder why? 
Hybrids always have the highest degree of heterozygosity... Hybrids sound like your ideal fish! 
Fastest way to boost heterozygosity in a population is a hybridization event... of course, those wild populations seem to have a lower mean fitness score than the pumpkin seeds in my parent's pond that can't outcross and have to avoid the bass daily...


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## NYjets51

Well you can not deny that inbreeding is bad in most animals. Not all fish inbreed in the wild.


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## MalawiLover

NYjets51 said:


> Well you can not deny that inbreeding is bad in most animals. Not all fish inbreed in the wild.


Yes we can deny it. How do you think we got all those different breeds of dogs, horse, cattle, etc. Why do almost all show quality schnauzers look practically identical? When done properly (meaning strict culling rules and only allowing the very best quality stock to reproduce) inbreeding actually improves the health of the end result offspring.


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## Number6

NYjets51 said:


> Well you can not deny that inbreeding is bad in most animals. Not all fish inbreed in the wild.


 It really only seems bad. It's impossible for me to deny inbreeding depression, but I strongly hold to the position that we do NOT understand enough about genetics to try to reduce the complexity down to the ultra-simple.

Inbreeding= bad is so simple that it is actually damaging to our breeding efforts.

All too often I read about someone who bought a male from store X and a couple females from store Y and think they just did a good thing.

Heck, I did that once... I had a bloodline of amazing A.jacobfreigi but after 5 generations, I stuck to the sage old advice of "time to outcross" and bought a new male. The fry from that pairing were drab and dismal looking. 
I was bitter...

So I began reading tons of info on genetics, breeding, etc. I also read the published papers sorted by date and it became quite apparent that a pattern was there...

1970- inbreeding bad
1980- inbreeding mostly bad
1990- inbreeding bad, but doesn't seem to be as bad in the wild
2000- inbreeding may not be all that bad. Outbreeding depression seems every bit as real. 
Today- genetic algorithms likely false as they are all built on assumptions of random pairing.

Current studies tend to conclude that there is a balance point appropriate to each species between inbreeding resistance and outbreeding resistance.

What is most interesting to me is that this balance point seems to be very different for every single species of animal out there!


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## narhay

MalawiLover said:


> NYjets51 said:
> 
> 
> 
> Well you can not deny that inbreeding is bad in most animals. Not all fish inbreed in the wild.
> 
> 
> 
> Yes we can deny it. How do you think we got all those different breeds of dogs, horse, cattle, etc. Why do almost all show quality schnauzers look practically identical? When done properly (meaning strict culling rules and only allowing the very best quality stock to reproduce) inbreeding actually improves the health of the end result offspring.
Click to expand...

And looking at all the health issues that specific breeds could have resulted from inbreeding depression. Bad backs in corgis, heart problems in cavalier charles spaniels...the list goes on.


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## 24Tropheus

I think the prob is we are trying to talk about all species as if there genetic make up was in some way the same.

Inbreeding can course problems in some species. So many dilaterous genes that become expressed that you can not cull (remove the individuals with unwanted traits) without losing the fishes look or some part of its behavior.

Many line bred animals have particular disease types and abnormalities due to inbreeding.

In other species they can do fine being totally inbred and largely identical.

You can find examples that tend to prove both arguments for and against.

Care full out breeding does not make any problems I know of (If the fish are genuinely the same regional type. A big if I grant you  )

Yes it can hide poor genes but thats a good thing, not bad surely?

I agree with the guy who suggested fish are pretty good at selection themselves when given the choice. But we will always need back breeding to wild ones every now and again. We select for fish that do well given the odd way we keep and breed them without trying.

If we want to keep them wild type looking and acting then we must select for this ourselves.
The fish can not do this they select for those that do best in aquariums.
To counter this we will always need wild fish every now and again.
Unless we want an identical fish line. (Not me)
It will differ from species to species how often this needs to be done. :-?


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## MalawiLover

narhay said:


> And looking at all the health issues that specific breeds could have resulted from inbreeding depression. Bad backs in corgis, heart problems in cavalier charles spaniels...the list goes on.


These problem are not really the result of the inbreeding, but of poor breeding techniques. The "backyard breders" who will breed anything with papers to make money and issues that occured before the whole genetics thing was really regulated well by the breed clubs are the root of the issue. Take English bull dogs. On average the bull dogs that are sold in the paper or that are sold by breeders designating them as "PET" quality (not to be ever bred) will snore something horrible and likely have soft pallate problem. If you go to the big dog shows, with the very high quality, carefully bred "SHOW" quality individuals you almost never hear so much as a wheeze. In fact the breed standard specifically talk about breathing.

Another prime exapmle of the uninformed messing things up is deafness in Dalmations. Here is an excerpt from the Dalmation Club of America Journal.



> The Dalmatian breed experienced a massive surge in popularity as a result of the 1956 novel The Hundred and One Dalmatians written by British author Dodie Smith, and later due to the two Walt Disney films based on the book. The Disney animated classic[10] released in 1961, later spawned a 1996 live-action remake 101 Dalmatians. In the years following the release of the second movie, the Dalmatian breed suffered greatly at the hands of irresponsible breeders and inexperienced owners. Many irreputable breeders and puppy mills cashed in on the breed's rising popularity, and began breeding high numbers of Dalmatians without first ensuring the health, quality, and temperament of the dogs being bred.


Even my own dog is a bit inbred, yet if anything I would say the inbreeding allowed the breeders to remove and screen out common maladies. My dogs father was bred back to one of his daughters. This occurs several time in his line and they have developed a line that no longer has the hip or eye problem previously associated with his breed. Infact his breeder is one of the top breeding kennel that are part of the AKC project to clean up the dog genome and to make the pure bred dogs of today geneticly stronger and heathier than the in the past.

It all comes down to if you do it right and know your genetics, it is not only ok, but often improve the species by breeding out problems that were previously caused by uncontroled inbreeding.


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## Number6

24Tropheus said:


> Care full out breeding does not make any problems I know of (If the fish are genuinely the same regional type. A big if I grant you  )
> 
> Yes it can hide poor genes but thats a good thing, not bad surely?


 Outbreeding depression is every bit as real as inbreeding depression.

When we outcross, we run the very real risk of obtaining incompatible alleles. The distance of the outcross matters significantly of course, but an outcross/hybridization event are all just shades of grey between what we call an outcross and what we call a genus level hybrid. 

There is also the very real effect of masking a deleterious allele and now spreading that disaster waiting to happen. 
Take fish that is a carrier for a deformed mouth gene. he has no deformed mouth but we cross him to a sister and all fry have deformed mouths... oh... bad.

Ok, so no we buy a new female and no fry have bad mouths. Of course 25% of the 50 fry have the crooked mouth gene and we just sold them...

so, take this 10 generations out there... all of a sudden, we buy fish from Toronto, Ontario and Chicago and boom... all fry have deformed mouths! Little did we know that number6 visits the GCCA auction!

Yikes says we... better outcross to WC fish... so we take our carrier, and outcross to produce 25% more carriers... good thing we know how to ship fish to California... they need good fish down there! :?


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## 24Tropheus

So we should cull all related fish to one that shows a genetic weekness or abnormality in any of its fry?

Not many fish would pass this test me thinks? :wink: 
Even WC pairs throw up some abnormal fry?

If we get rid of all poor genes we must then continue to produce pure lines 2 and then cross these?

It will not happen for most fish the best we can do is keep em as wild type as we can I think.


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## Number6

24Tropheus said:


> So we should cull all related fish to one that shows a genetic weekness or abnormality in any of its fry?
> 
> Not many fish would pass this test me thinks? :wink:
> Even WC pairs throw up some abnormal fry?
> 
> If we get rid of all poor genes we must then continue to produce pure lines 2 and then cross these?
> 
> It will not happen for most fish the best we can do is keep em as wild type as we can I think.


Nope... the good news is that the fish are self correcting if you let them be so! 
If we spent less money trying to buy WC or F1s (especially from two sources or more) and simply bought much larger groups in a much larger tank, then what we shock ourselves with is finding that your percentage of deformities drops to nil or almost there and you didn't do anything!

Like I've said... it's so weird you'd think these fish had an instinct for it or something :wink:


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## 24Tropheus

Well I guess we agree on that one for mouth brooders.  
I still think there is a place for WC fish. But not to improve bad stock. (sorry if I suggested this not my intention) 8) 
Sadly nearly all the stock of aquarium Malawi cichlids here is so very poor, I think its best to start again with WC.
Most of the fish available are 
1 Not pure.
2 Bred by folk with small tanks and small numbers of fish. (often containing multiple species or regional types)
3 Cheap imports of poorly bred fish (no selection)
or
4 Stripped lines.

It would take many generations of good breeding to make anything good out of this mess.


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## MalawiLover

24Tropheus said:


> Well I guess we agree on that one for mouth brooders.
> I still think there is a place for WC fish. But not to improve bad stock. (sorry if I suggested this not my intention) 8)
> Sadly nearly all the stock of aquarium Malawi cichlids here is so very poor, I think its best to start again with WC.
> Most of the fish available are
> 1 Not pure.
> 2 Bred by folk with small tanks and small numbers of fish. (often containing multiple species or regional types)
> 3 Cheap imports of poorly bred fish (no selection)
> or
> 4 Stripped lines.
> 
> It would take many generations of good breeding to make anything good out of this mess.


I am not sure what you mean by #4, but the rest sounds like you have hit it on the head. Without serious culling, and some bringing in of healthy blood to correct the rampant flaws in many aquarium strain, those aquarium starins of some species are going to burn themselves out. If only we had all know about this 20 or 30 years ago, all the fish at the LFS would be amazing..


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## Number6

*24Tropheus*
Totally agree! Excellent reasons for buying WC or F1... I might even be so bold as to say that those are the only reasons I can mentally justify paying for WCs.


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## Kanorin

I had posted another thread about inbreeding genetics and someone kindly pointed me here, so I'll dredge this one up rather than having the same discussion over again.

It seems that breeding cichlid lines over a few generations should not be a problem, as far as fitness and health go, so long as any "misfits" can be culled by the breeder.

However I have also come to this conclusion. Given wild caught Fish A,B,C,D -which are all the same species, the F5+ (5+ generations of inbreeding) offspring from wild caught Fish A and Fish B may be quite a bit different from the F5+ offspring from wild caught Fish C and Fish D. I suspect that there are two ways to look at this:
1) This line variation makes each strain somewhat unique, thus desirable. This also rewards "good breeders."
2) This line variation is unnatural and neither of the inbred strains are truly representative of the wild species.

That being said, buying a male from source X and female(s) from source Y is not natural either. The only way to achieve natural breeding and genetics is to leave them in the lake! (But that's not fun for us  )


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## Number6

Kanorin, inbreeding helps to fix traits... those traits can be the "wild look"... it all depends on what is selected for by both fish and the person controlling the bloodline.


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