Inbred Mistakes I

There’s a lot of bad information about inbreeding out there, most of it generated by breeders who are grasping at straws to defend the process they have been told is their best and most useful tool to shape their lines.  This misinformation campaign is so common that even enlightened scholars on the subject have incorporated some of the lies into their understanding.

Before I tackle some of the most grossly inaccurate propaganda pieces, I want to correct a few minor mistakes in an otherwise excellent analysis on inbreeding and the breeder culture.

The essay you should check out is Joanna Kimball’s Inbreeding and COI post at Ruffly Speaking. Joanna provides a great insight into the mentality of the show breeder and why they want to use inbreeding and how they make it part of the culture.  We do it this way because we’ve always done it this way.

The highlights are too numerous to repeat here, so I will instead offer the following minor, but important, corrections.

Line-breeding is still inbreeding, but we give it a different term to show that we’re not just concentrating genetic material randomly (as you would if you bred brother to sister). You’re doing it to try to re-create the aspects you like of a single dog or group of dogs in the pedigree.

While the first part of this statement is true, close breeding isn’t necessarily random, certainly not more random than line-breeding more distant relatives.  Selection vs. randomness is a different quality that can be applied to a brother x sister, father x daughter, or more distant pairings.  Randomness would imply that we are not selecting, but breeders almost always select.  As I wrote about before, inbreeding by itself doesn’t change the frequency of alleles across the offspring, it simply creates more AA and aa individuals versus Aa individuals.  It concentrates and separates, but by itself it does not exclude.  Breeders using selection do the exclusion; the concentration of alleles makes each individual selection more potent in removing diversity.  And no breeders inbreed and then use all the offspring equally, as this would defeat the goals behind the inbreeding.

This would be similar to a brewer distilling a 50% alcohol-water solution into 75% alcohol and then adding the removed water back in.  The process of distillation doesn’t destroy water or alcohol, it simply gives us two solutions that become more concentrated alcohol and more pure water.  It is the selection of the alcohol and the removal of the water that removes total “diversity.”

Breeding brother to sister is not more random than a great-grand father to great-grand daughter, it’s just more likely to double up a greater percentage of alleles.  If we are selecting for the same apparent trait in both cases, say chocolate coat color, the brother x sister pairing will not result in more random results on that trait and all other traits that the two parents share.  In fact, we are more likely to see more “randomness” in the non-selected traits in the distant mating than in the close mating because a brother and sister are already expected to share 50% of the same alleles.

I think what Joanna is trying to say is that closer breedings are more likely to double up on genes that the breeder has no desire one way or the other to be doubled up. This is true, and this is why a more distant breeding between dogs that still share the desired traits is safer.  In fact, this is what I advocate.  If you want to maintain good bone and a long shiny straight coat in your dogs, find an unrelated dog that has both good bone and a long shiny straight coat.  This should not be that difficult, and the benefits to keeping the other 99.9% of the genes that we don’t want doubled up on unnecessarily free to be heterozygous is a major benefit.

You can keep pushing COI further and further back, but at some point it becomes less useful because you start hitting the founding dogs of the breed and that can artificially inflate the COI (because those are behind every single dog in that breed). So ten generations is considered pretty standard.

This is not true.  Adding more information to a COI calculation is NEVER less useful or less accurate.  The truth is the exact opposite: looking at only a few generations can give you the mistaken impression that you are not inbreeding.  Taking a COI calculation back to the founders and beyond will never “artificially inflate” the COI.  The opposite is true. Once we reach a founding dog (i.e. a dog that we know nothing about its parents) we have created ARTIFICIAL DIVERSITY.  The COI calculation assumes that all founding dogs are 100% unique and 100% heterozygous.  We know this isn’t true, it’s never true, but it’s an assumption we have to make.

If you only have 8 generations of ancestors, and you take a COI(10) or a COI(100) the answer will be the same. There’s no inflation, no distortion, and no creeping artificiality.  The Coefficient of Inbreeding calculation has an exact definition and that definition in no way becomes less accurate the further back you go.  COI is both the probability that two alleles in an individual are identical by descent and also the proportional decrease in heterozygosity under inbreeding.  The more we know about the ancestors the more accurate and representative the COI calculation is.

Failing to go back as far as you can ARTIFICIALLY DEFLATES the COI calculation.  A dog can not be found to be less inbred by finding out more about its ancestors. It can only be found to be more inbred.  All the dogs in the Nth generation of a COI(N) are assumed to be unrelated and heterozygous.  No additional information can make that any less extreme.

The reason that a COI6,7, or 10 is more “standard” practice in the breeding culture is not accuracy but convenience.  The amount of information and the difficulty of calculation doubles each generation requring the use of expensive software and burdensome data acquisition and entry.

It has taken me over 4 years to compile the near-complete pedigrees on my dogs and even then I am stuck at a few dead ends in now-closed registries.  It has taken literally thousands of hours of phone calls, letters, faxes, and e-mails and inquiries into online databases and to other breeders to compile copies of pedigrees and information from stud books.

If we count the single dog as the 0 generation, the parents as the first generation, etc., then a 10 generation pedigree will have 2047 potential dogs on it.  While one page can hold a 5 generation pedigree with 62 ancestors on it, you’ll need to collect 33 such pedigrees to fill out a 10 generation history.

The worst error, however, comes in the comments to Joanna’s post where a breeder named Todd Chrisman says this:

While I agree with you generally, your take on COI is off. Outcrossing decreases “genetic diversity” by melting all of the strains and family types of a breed into one pot. The problem is you gloss over the negative recessive traits and those traits come back to haunt your breed, you have no repository of “clean” genetics to turn to.

This is bunk. As I noted before, inbreeding or outcrossing by themselves do not increase nor decrease genetic diversity.  They only change the degree to which the existing alleles are segregated into like alleles.  If we blindly inbred dogs over several generations with no selection other than relatedness, we’d find that the numerous puppies would be highly inbred but that we would have the same representation of alleles as the original founders.

This of this like a deck of cards where every two cards represents and individual.  A mostly heterozygous gene pool is a randomly shuffled deck.  A mostly inbred and homozygous gene pool would be a deck that is fresh out of the package with almost all the red cards next to red cards and almost all the black cards next to black cards.  In both cases, there are 50% red cards and 50% black cards, but under inbreeding we have many many more pairs of cards that match color.

Instead of being well mixed and heterozygous, we would find most alleles paired up and homozygous in the highly inbred lot.  For example, if the two founding dogs were Aa x Aa, we’d eventually find that all the puppies would be AA or aa.  All those puppies would not be clones, however, as their other genes would be homozygous but not paired equally.

If the parents are Aa Bb x Aa Bb, the offspring would eventually be: AA bb, AA BB, aa BB, aabb.  So all the offspring are homozygous, but we still have 50% As, 50% as, 50% Bs and 50% bs.

In practice, breeders breed very few puppies from each litter and continue to inbreed upon them.  This throws out genetic diversity as fast as you can.  To maintain genetic diversity, one needs to not only breed unrelated dogs, but you also need to use multiple puppies from any give pairing instead of just a few.  Any given puppy is only able to preserve half the genes from each parent.  The more heterozygous the parents, the harder it is to preserve their complete genome.

The bogus “melting” concept Todd presents has no support in biology.  It is just the opposite. A heterozygous dog is able to preserve twice the data than a homozygous one as I have demonstrated in a previous post.

So too is the idea that inbreeding can maintain a repository of “clean” genetics that can be used to save the breed is as well unsupported by any physical means or observationally.  Normal genetic drift, let alone consistent and breed wide selection on a few criteria lead to the rapid change in the frequency of gene variants; in other words, the concentration and loss of genetic diversity.  In general, alleles drift to loss or fixation [appearing in none of the breed or in all of it], and this happens significantly faster in smaller populations.  A frequency of 100% does not mean that genetic drift leads to homozygosity, rather that at least one of the possible two alleles will be the one in question.

This is why, for instance, flat coats and goldens are no longer produced in the same litter, why there are no Dalmatians without spots (or a uric-acid stone problem), and why fluffy corgis are on the way to extinction.  The popular sire effect and the selection of only a few sires to produce the vast majority of puppies in breeds has made the notion of truly distinct lines a fantasy.

If there is an inbred pool of “healthy” dogs, it is to be found in another breed, and even then the rules of blood purity have prevented the Dalmatian backcross project from being accepted. And the idea that an outcross needs to be inbred itself is also unsupported and dangerous.  One never need turn to this mythical healthy inbred population if breeders would simply outcross and bring in even a little bit of new blood.  The maximum benefit will not come in removing disease through inbreeding (this has never been successful), but in managing disease so that it is rare.

It is not a problem that disease exists in dogs, it is a problem that it is so prevalent.  Playing the lotto is not stupid because you have a chance at winning a fortune, it is stupid because you have a really really really lousy chance at winning and a very very very good chance at losing your investment.

Negative recessive traits don’t come back to haunt outcrossed breeds. They remain rare and unexpressed. They are harmlessly carried, affecting very few individuals, until normal genetic drift removes them.  They only haunt inbred breeds where they are doubled up on and are carried by genetic drift to 100% frequency instead of 0% frequency.  This is why sickle cell anemia and Tay-Sachs disease are very rare in the greater human genome but highly concentrated within certain ethnic gene ponds.

Todd Chrismann’s analysis is idiocy.


I’ll continue this series by looking at breeders very different from Joanna, who are actually trying to spread misinformation or whom are expert at convincing themselves of lies that would allow them to continue their time-honored but destructive practices without having to come to terms with reality and the harm they are doing.

Inbred Mistakes Series: (1) * (2) * (3) * (4) * (5)

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About Christopher

Christopher Landauer is a fifth generation Colorado native and second generation Border Collie enthusiast. Border Collies have been the Landauer family dogs since the 1960s and Christopher got his first one as a toddler. He began his own modest breeding program with the purchase of Dublin and Celeste in 2006 and currently shares his home with their children Mercury and Gemma as well. His interest in genetics began in AP Chemistry and AP Biology and was honed at Stanford University.