Posts Tagged ‘popular sire effect’

It would take just 50 random ISDS border collies to reconstruct Wiston Cap.

No popular sire problems in BC’s?

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Jess at DesertWindHounds discusses the importance off genetic diversity in the Major Histocompatibility Complex (MHC),  a gene family that controls immune responses. In dogs, it’s called the Dog Leukocyte Antigen (DLA) system

It’s very important that everyone in dogs understands these concepts.

In fact, it’s very important that everyone interested in conservation of endangered species or in breeding any kind of animal has a full grasp of the problems that can happen with reduced diversity in the MHC.

This angelfish website also partly discusses the MHC. Unlike Jess’s post, it is pro-inbreeding, but the author recognizes the need to bring new blood in.

The problem with dogs is we are operating within a closed registry or a Potemkin open registry system where new blood is not easily brought in.

And with virtually all Western breeds, all individuals within a breed are derived from the same founders.

The is the big problem with line-breeding, inbreeding, and using just a few sires  per generation within a closed registry system. At some point, the breed becomes too homozygous within the MHC/DLA, and it’s screwed when a really bad disease pops up.

My guess is we’re going to hear a lot about the MHC in the near future. Many success stories of recovering endangered species are going to turn into disasters.  Some species have recovered from a very low founding population, and that means that they don’t have much variation at all in their MHC.

That’s bad.

And there is one animal right now that recovered from intense persecution in its homeland. It was eventally protected, and its numbers grew.

But now because of a communicable disease, it may very well go extinct. As a species, it has low genetic diversity and very little variation in the MHC. If it does become extinct, it will be this compromised genetic diversity that ultimately does it in. If it had more diversity in its MHC, then some individuals might have a some immunity to it, but thus far, all have been found to be highly susceptible to this disease.

I’ll reveal that animal and its disease  tomorrow in a longer post.

Until then, read this post and get a good understanding of what the issues are.

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The popular sire is not limited to dogs or even common domestic animals. It is a problem that plagues a wide array of species that are bred in captivity.

Domestic dogs have a wealth of genetic diversity, and although much of it is sequestered in various breeds and strains, it is generally fairly easy to produce healthy puppies.

Dogs are the oldest domestic animal, and they descend from a wild ancestor that was quite widespread. That means that as a species, dogs would (and should, in theory) always have enough genetic diversity to produce viable offspring.

But what about species that have only recently been bred in captivity?

What about those species that have a much narrower range and only a very small founding population?

Such is the case when the Centre for Fortean Zoology began breeding a Guatemalan livebearer, Scolichthys greenwayi.

Unlike wolves, these fish are native to only the Rio Chixoy or Rio Salinas river system in Guatemala. That means that attempts to produce “domestic strains” are dependent upon imports, and imports are necessarily quite small populations in relative terms.

To make things even more complicated, these fish are typically harem-bred, with one male servicing six females.

And that’s where the popular sire effect takes place.

When the Centre for Fortean Zoology purchased two pairs of these fish at an auction, it looked like they were going to have the start of a successful breeding program.

As their name suggests, livebearers give birth to live young that hatch from eggs that are retained within the female’s body.

The particular livebearers produced offspring within two weeks of being introduced to their new tanks, and it was expected that these little fry would do well.

The Centre’s tanks are set up with weeds for the fry to hide in, and this allows a certain amount of natural selection to go on. The fry hide within the weeds to avoid being eaten by their parents or other fish within aquarium. Fry that cannot do this very well are eaten.

(This is very different from the way I remember seeing swordtails bred. The “pregnant” females are typically placed in a breeding trap, which is placed in a nursery tank. The female is placed in that trap, and when she gives birth to her fry, they escape through tiny holes on the floor of the breeding trap, escaping their mother’s jaws. It allows the breeder a chance to select which offspring survive.)

The Guatemalan livebearers produced several “clouds” of offspring throughout the summer, and hopes were high that the tank would soon be full of fish.

However, months passed, and no small fish came swimming out of the weeds.

Upon inspection of the weeds, no fry were found, but one horribly deformed juvenile was discovered . The spine was twisted in a “S” shape. Upon more careful inspection, a few more juveniles were found– all with this deformity.

Careful checks of the tank chemistry found no abnormalities.

The problem could only be genetic, as Oll Lewis writes:

The problem stems from too much inbreeding leading to a small gene pool which means genetic problems can become magnified within the population. Small fish are often prolific breeders and will produce lots of young, which is fine when they live in a large river and it is likely that there will be lots of other fish with different genetic lineages just down the river to breed with but in captivity often closely related fish will breed with each other meaning the available genes are reduced. Often the fish that look outwardly fine are selected for further breeding or sale and the ‘rejects’ euthanised, but a fish can easily be carrying the genes that could contribute to deformities in their offspring even if the appear to be fine. Other things exacerbate the problem and can speed up the shrinking of gene pools such as selling fish to other collectors with a much larger number of one sex than the other. For example if you were to attempt to breed using one male and six females you’re going to reduce your gene pool very fast indeed. I have actually seen evidence of a few scolichthys greenwayi being sold in similar ratios online so it is easy to see how the captive genetic stock can be reduced quite fast. In order to counter this many of the more responsible breeders will buy in adults from other breeders to attempt to counter this, but often unless you know the full lineage of the fish you might be just adding inbred stock. Zoos and conservationists have been aware of the problems inbreeding causes in a population for a long time and accurate stud books are kept for most animals to ensure that, when breeding, genetic diversity is maintained. Some fish breeders will keep stud books but often hobbyists and some commercial breeders will not and because of this it often becomes near impossible to keep a studbook only a few generations after a particular species has been introduced to the pet trade.

In other words, popular sire effect.

Now this problem could be solved using two methods.

  1. Import new stock from Guatemala, if this is indeed possible.
  2. Use breeding stock from different breeders.
  3. Breed from more males.  Keep a higher ratio of males to females in a breeding population

Of course, people who breed livebearers are always trying to breed “pretty.” I’m sure that using just a few males as breeding stock is a good way to ensure that only the most attractive fish produce fry. No one wants to buy homely fish.

It’s the same thing that happens in domestic dogs, whether they be show or trial stock.

Of course, with dogs, we have the ability fix things rather quickly. It is merely cultural reasons that we don’t work to solve our problems with genetic diversity.

With these fish, one is reduced to working with what one has. I’m not sure if these fish are currently being collected in the wild, so it may be impossible to get new blood.

And the vast majority of these fish breeders are in the mass production business. No one really traces the bloodlines. It’s about producing fish at volume, regardless of the health of the gene pools– or the long-term health of  the fish.

These fish have very short generations and are prolific breeders, so it would be hard to set up really clear bloodlines.

But is clear that the popular sire effect causes problems in fish.

What happened with these livebearers should be a warning to us about what could happen if we aren’t careful about genetic diversity.

It can mean severe consequences.

The story of these fish should put everything in perspective.




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What mechanism drives the popular sire effect?

The answer is complex, but in the end, it can be reduced to two simple quests:

Breed for superman and breed from superman.

One of the most interesting factors that drives the most used sire effect is something called “prepotency.”  That’s the ability of a sire to produce quality offspring over a wide range dams. The only way to prove this ability is to breed to as many dams as possible.

On the Border Wars blog, Christopher Landauer, explains that

[t]he greater theory of Prepotency is bunk: that superman sires should be able to overcome any problems in the dam, ideally the female being but a vessel to produce perfect copies of the sire.  What isn’t bunk is the very real effect of rising homozygosity: the more homozygous the parent, the less variation in genes passed along to the offspring.

The culture celebrates stud dogs. Simply because a males can have many, many more offspring that females, sire have a greater influence on the gene pools than dams do. If one has a great stud dog that has superior traits in either phenotype or behavior, one has the ability to affect the greater development of the breed as a whole.

The owner of a good stud dog has great power, and with this power comes responsibility.

As a whole, this problem has not really been given careful consideration within the various fiefdoms, principalities, and cliques with the greater dog culture.

The goal is to produce that superman dog. One that has such superior traits in whatever utility he is needed for and to have him replicate those traits when bred to so many different bitches.

That is where power comes from within these dog culture systems.

If you have a stud dog that is totally awesome, one can really control the breed–for more than just the present generation.

Top producing sires are quite feted, at least within the AKC system. (Here’s the record for AKC St. Bernard sires. The healthiest breed ever, right?)

That is a problem.

So how are we going to solve this problem of the popular sires?

There are some answers, but they are almost all contrary to the prevailing wisdom and cultural mores inherent within these systems.

Line-breeding and inbreeding are the best ways to produce offspring that are relatively similar in whatever way one desires.

It takes a bit more skill to produce the exact qualities in more heterozygous stock.

And we can’t mention the idea that we might want to open registries to allow new blood in.

That idea is either universally p00-pooed as it is in the big multi-breed registries or  given lip service as it is in the JRTCA and ABCA, which are, for all intents and purposes, Potemkin open registries.

The only real open system with dogs is one that exists for racing sled dogs, which doesn’t even have a central registry system. You simply breed what runs hard and long  in very cold conditions with what runs long and hard in cold conditions. That really doesn’t exist anywhere else in the greater dog culture, although the feists and curs still exist within something like it, even as they are all being standardized into breeds.

Domestic dogs possess great genetic diversity. However, in the West, it has been sequestered into various breeds or strains. (In the East, well, as we have seen in China and Japan, they have simply adopted the Western system.)

Besides opening the registries, we have lots of things we could do but are so politically impossible to do on a large scale.

The notion that we should really worry about how genetically diverse the various bloodlines are is simply a major affront to the prevailing wisdom.

Diversity means less predictability.

I have read dozens of dog books that extol the main virtue of the purebred dog: we know what we’re getting when we pick a certain breed.

That means that somewhere there must exist a happy medium between preserving genetic diversity and producing dogs that have a relatively consistent phenotype and temperament.

I think the answer may lie with the boxer/corgi hybridization program. There a naturally bob-tailed corgi was bred to white boxer. And within just a few generations of breeding back, dogs were produced that looked and acted just like boxer. But they had natural bobtails. (With country after country banning tail docking, is this really such a stupid thing to consider?)

If a breeder can do that with two breeds that are as different as boxers and Pembroke corgis, then one surely would be able to produce a consistent phenotype  and behavior with the use of two similar breeds.

Just a little variance on just a few genes separates the different dog breeds. It is one reason why dogs change type over just a very short period of time. It is also why wild wolves vary so much in appearance and have always done so.

But it is hard to think like this, when the culture is all about breeding for superman and breeding from superman.

To have a superman means that one’s breeding program is immortal.

To breed from a superman means that one gets a bit of the super gene and over time, the breed will become more consistent in type and temperament.

Until the inbreeding depression sets in.

But that’s as long way off.

It is better to have results as soon as possible. That’s how one wins. That’s how one gets closer to immortality within the breed.

This is the quickest and surest way.

The other way, well, that requires a  some more work, a little bit more study, and lot more commitment to actually produce. It requires tolerating some variance and maybe a bit of mediocrity to reach a better goal.

It is not a short-cut. It is the harder way.

Which is why the number of breeders who actually consider genetic is actually quite low.

It’s not the fastest way to breed for superman.


Everyone should check out that post at Border Wars, not just for the discussion of prepotency, but for the really good graphics that explain what inbreeding is and what it does to the population.

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