Genetic bottlenecks, environmental pressure, and the development of dog breeds

I read MANY blogs. Somewhere in the range of a couple hundred. News, photography, scrapbooking (to make me feel guilty), and of course animal behavior, sheltering, all the Cardi blogs, legislation blogs, Gizmodo and Freakonomics and Lifehacker and Dooce, etc.

Some I read to keep me honest–Nathan Winograd is good at that.

Some I read because deep down some part of me wishes I lived the life of that blogger–the Daily Coyote comes to mind.

And there’s one I read because after I read his stuff I have to turn off the computer and go stare at the sky. Stephen Bodio is a hawker, a dog owner and breeder, a cattle rancher, a man who has dust in his boots and an incredible amount of deep and true thought in his head.

He wrote recently and touched on a few of the current genetic arguments surrounding dog breeds, which I thought dovetailed neatly into what I’ve been talking about in terms of genetic diversity in breeds. So I’m not going to quote him but I am going to use a few of the example breeds that he brought up.

Breeds as landraces are very, very old. A landrace is just as useful as a breed but it tends to be defined solely by the job it can do and by its environment–if you think about the Border Collie before it was ever registered, you get an idea. Their appearance can vary–if you mean appearance like “show quality” you could say the appearance varies a lot. Some Border Collies are substantially larger, some smaller, some have prick ears, some drop, color and coat type and leg length can vary. But in many other ways they are very similar–most people can still reliably identify them as Border Collies, and they all work in basically the same way.

The difference between a landrace and a breed is that a breed generally has a closed population, where individuals are bred only to other members of that breed. When you’re working with a landrace utility is king–if a dog shows up that kills rabbits really well, you’ll want to keep him around to breed to your other rabbit-killing dogs even if he doesn’t look exactly like them. But he’s unlikely to look totally different from them either, because there’s a certain body type and size and speed that naturally lends itself to successful rabbit killing. So among landraces there is a certain amount of sharing of genetic material–if the rabbit killer also happens to be a decent fox chaser, he may be used by people who like chasing foxes too.

Landraces probably developed along the same lines that dogs became domesticated hundreds or thousands of years prior–the dog wanted it and the human wanted it, and dogs have a tremendously plastic body and brain and from that symbiosis came dogs that were more useful at doing certain dog-human things than their ancestors had been.

So very, very long ago we can see what we think of as the major types of dogs. The Far East pioneered the idea of the dog purely as a companion, and they like the very stylized appearance of the flat-faced small dog, and so the flat-faced companion dog begins to spread along the trade routes coming west. This was happening thousands of years ago–the flat-faced small companion dog is very ancient.

Another group, probably in Germany, liked a type of dog that had very short legs, because short legs enabled the dog to do some things that long-legged dogs could not do. They probably began using them as hunting dogs but when the trade and conquest routes brought the short-legged dogs to other areas where hunting was not the predominant activity that dogs did, the owners of those dogs realized that short legs made some of their activites easier and made those dogs very useful. So, and again this is thousands of years ago, we already have a corgi landrace herding in Wales, a Vallhund landrace herding and hunting in Scandinavia, a Dachshund landrace hunting in Germany, etc.

The earliest true breeds, where pedigrees were maintained and it was understood that you only breed members of that breed to each other, are also extremely old. They grew out of an increased specialization of the landraces, a desire to have greater predictability in terms of exactly how big, small, tall, short, or useful that dog was.

There are only a very few of those true early breeds still around. Most of the breed-origin myths that are droned over the picture at Westminster are romantic fiction. But some of them DO still exist. One is the Sloughi (not Saluki), one is the very primitive Basenji, another is the Chow, and I think the Pekingese makes the list as well.

So the vast majority of the breeds we know today became closed, where individuals were not bred outside the breed, only in the last couple hundred years. It’s important not to therefore conclude that all dogs looked the same before that point, or anything close to that. If you traveled through Europe in 1600, you’d see an incredible number of distinct-looking dogs and probably hundreds of what we’d call breeds. But there was still communication between the breeds, sometimes slight and sometimes heavy.

When identification of breeds and registration of individual dogs, and eventual closing of studbooks, became fashionable in the 1800s, two things happened: Existing breeds were identified and codified and registered, and older breeds that were seen to be in danger of extinction or in come cases had already become extinct were re-created. So the Ibizan Hound and the Pharoah Hound were re-created, as were the Irish Wolfhound, the Elkhound, and many others. It seems unlikely that any of these were created from absolutely nothing; it’s a lot more likely (and certain in a few of them that I know the history of) that people passionate about a disappearing breed or landrace gathered the last remaining members of the population and then bred them to dogs that were as similar as possible to them in appearance and function.

At any rate, we have between 1850 and 1900 a whole ton of breeds being gathered, registered, and from then on bred only to each other.

By the 1930s there are a whole bunch of breeds that have their stud books closed (in other words, no more dogs are ever going to be let in).

Here’s where it gets sticky. In the 1920s and 30s distemper was killing dogs off in huge numbers. And then the advent of World War II and the extreme levels of starvation and hardship in Europe dealt a horrible blow to a large number of dog breeds.

Sussex Spaniels, for example, almost completely died off or were killed. The population dropped to just eight individuals. Shar Peis dropped to incredibly small numbers even more recently, as of the late 1970s. Lundehunds were reduced to six total. Cavalier King Charles Spaniels almost disappeared and were only saved by intense inbreeding in the 40s. Flatcoat Retrievers almost died out as well. The list of breeds that was reduced to only a bare handful of individuals is pretty long.

This is the definition of a genetic bottleneck. If, after the event or environmental pressure that kills off the vast majority of the population is over, no more founding individuals are added, then the entire breed (or, in the case of certain animals like the Asiatic lion, the entire species) becomes an expression of only those six or eight or whatever individuals.

A founding population that is that small is extremely risky. The likelihood that you can develop a genetically diverse and healthy ongoing population from six or eight or twelve already related members is small.

And, in fact, we do see that risk played out in these breeds. Sussex with their low fecundity and heart issues, Cavaliers with heart and brain problems, Lundehunds with mysterious digestive issues and early deaths, Flatcoats with cancers that effectively cut the breed’s lifespan in half.

So we have moved, in most breeds, from a situation of quite a bit of genetic information coming into and leaving the landraces to gene pools that are entirely based on a startlingly small number of dogs and where zero genetic material comes into or leaves the population.

We have effectively made each breed into an endangered species.

I can tell you, from far too many late nights up studing population ecology, that one of the things that is considered an immediate emergency in an endangered species with no available genetic material from the outside is keeping the heterozygosity of the population absolutely as high as it can be. It is considered so critical that the at-risk populations are constantly monitored for COI and also a direct measure of heterozygosity called MLH, and increasing heterozygosity is a key sign that the population has hope and may succeed and survive.

There are very few, if any, endangered species experts monitoring dog populations. That’s because the “dog” is not in any way endangered. Taken across the whole world it’s in great shape. But don’t fool yourself into thinking that individual breeds are not at critical danger of collapse and extinction. Both in absolute numbers and in size of gene pool, there are a strartling number of breeds that should be considered critically endangered. Even in the more numerous breeds, the representation of founding members is extremely poor and the average mating is equivalent to full-sibling.

If we don’t pay attention to this, we WILL pay the price, or the next generation of breeders will pay the price. I don’t know how much more plainly to put this–we’ve been breeding in a way that is very unlikely to be sustainable. And since we’re the ones making the decisions, it’s up to us to do our best to fix it.

High coefficient of inbreeding and disease

One of the things I’ve read recently by a breeder of a different breed (not Cardis) is that high COIs are absolutely essential to keep disease from spreading through a population.

Here’s how that line of reasoning works.

If I have a population of dogs that does not have Spotted Snarkle disease in their pedigrees, and I know that, I should keep breeding those dogs only within their own lines because breeding outside their lines will spread Spotted Snarkle disease.

The logical outcome of this is that the entire breed becomes very segregated, with some lines “known” for Spotted Snarkle disease, others for Awl Border disease, others for Maniac Mouth, and so on.

Increasing the genetic crossover, the exchange of genes between these lines, is therefore “dangerous” because then ALL the lines have all three diseases! Oh noes!

Here’s why that’s wrong.

Let’s create two populations.

Population A has a thousand dogs. 900 of them are free from Spotted Snarkle and 100 of them have pedigrees that are “known for” it. Of the 100, fifty are carriers of the disease and 25 actually have it. Every dog who actually has Spotted Snarkle is culled. The populations are rigidly separated.

Total population year 1: 1000

Incidence of Spotted Snarkle: 25

All affected dogs are culled, but the carrier population remains segregated. As a result,

Total population year 2 (assuming identical numbers of births and deaths): 1000

Incidence of Spotted Snarkle: 25

Population B has a thousand dogs. 900 are free from Spotted Snarkle and 100 are in pedigrees that are known for it. Same situation; fifty carriers and 25 affected dogs. The populations are allowed to freely interbreed. Again, all affecteds are culled.

The 50 carriers move out into a population of 925 other dogs. Therefore, the chance of a carrier meeting a carrier moves from 50% to around 5%.

Total population year 2: 1000 dogs.

Number with Spotted Snarkle: 2.5

So has Spotted Snarkle moved out into the whole population? Yes. Is the population still better off? YES. There are many fewer affected dogs; the problem has radically improved.

That’s how maximum genetic diversity works. Even though the incidence of deleterious genes is wider spread, the chance of identical deleterious genes meeting is MUCH lower than in an inbred population.

Proponents of high COIs and rigid segregation of lines forget some very key population truths.

One problem is that they’re assuming “success” based on only a tiny, tiny, TINY fraction of the number of diseases, genetic disorders, and weaknesses that actually exist. You can’t claim success if you’ve avoided Maniac Mouth when you have no idea what other 500 genes you’ve concentrated in your little insular population. High COI is not just associated with creating or avoiding the “sexy” diseases, the big flashy ones like Addison’s disease. It’s associated with an increased risk for low-grade, old-age, late-onset diseases. Mastitis. Kidney disease. Smaller litter sizes. Lower growth rates. Senility. Worms and other parasites. Vitamin deficiencies. Lower resistance to infections. The list is VERY long.

The second, and most sad, of the things that advocates of high COI ignore is the fact that breeders lie. They lie a LOT. I am thankful to have mentors in both Danes and Cardis who have been honest with me, but by the end of my time in Danes I could have written a book about breeders lying about pedigrees and about health. I hope things are different in Cardigans, but when when I was breeding my last Dane litter and was looking at pedigrees of stud dogs between a third and a half of them I was rejecting because I knew that at least one dog, or one health result, was false or at least very suspect. The tragedy of this, beyond the moral downfall of that breeder and the sadness and pain she causes to everyone who breeds based on a lie, is that you really can’t count on your “safe” pedigree. Not to any great extent.

If the goal of an entire breed is to keep COI low, the overall incidence of disease will be lower even if you were deceived in a pedigree or by a breeder (or that breeder’s breeder, ad nauseam). You will keep disease expression lower across the board, protecting future generations from the hundreds of diseases we can’t test for and that don’t make the headlines. And you will keep the population’s ability to respond to new, unknown threats at its highest level.

Another, more sentimental, benefit from my point of view is that spreading genes around keeps you concerned about the whole breed, and links you to and bonds you with many more breeders. It keeps the world small. You won’t be as willing to cut people down if you know they’re part of your pedigrees and you’ll be concerned with the eradication of disorders across the whole breed because your dogs participate across the whole breed.

Commentpalooza part 2: Inbreeding dogs (redux) and a whole bunch of bolding.

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.

I totally agree that breeders need to know what they are doing and why they are doing things. You can’t ethically breed dogs by following a recipe, and you should have a strong idea of where you are going not only in this generation, but for several generations to come.

Please Google “Of Peas and Pups” as it is the best free source of information on the topic.

Hoorah! I get a chance to re-address this topic.

Let me say first that I am thrilled beyond belief to see any breeder making decisions based on more than just “Well, her grandfather had two BISS wins, and I certainly want a piece of that, so I think I’ll breed to him.”

The article “Of Peas and Pups” was written in ’63 by a German Shorthair Pointer breeder who was very influential in the breed. It is ABSOLUTELY worth reading. When I summarize it, I’m doing so not because I don’t want you to read it on your own.

Of Peas and Pups is maybe the best example out there of the reasons that breeders stick within very, very tight pedigrees. The point of the article is, in short, predictability is good. Maximum predictability is better. Perfect predictability is best of all.

This is a quote:

We also learn that only pure parents produce pure offspring…Our dogs of course, are not genetically pure and never will be, but whatever minute contribution we can make toward that goal of genetic purity, will be to the everlasting advantage of the breed in the generations to come….

We can see that (in most instances) hybridizing or outcrossing , whether it be of breed or strain or type, complicates our genetic arrangements…..Ideally, we want HOMOZYGOSIS or the homozygous state for every allele. This is a dream not to be realized unless this old world spins a lot longer than it has already.

The author gives examples of the things you want predictability on. Nose, instinct to run, size, shape, fearlessness, etc. He strongly asserts that if you do a lot of outcrossing (breeding to unrelated dogs) you may get a few really able dogs but you won’t be able to reliably count on the outcome. You’ll be breeding somewhat blind because the dogs will be quite different from each other. Maximum homozygosity (where all the genes are the same, no recessives–or ALL recessives, depending on the gene you’re talking about) leads to maximum predictability.


This is EXACTLY my point. Only I want you to imagine it like this:

You’ve got seven three-foot lengths of yarn in a rainbow pattern. There are lots of colors in repeating patterns down the entire length, in a random order (so sometimes it’s blue-red-orange, sometimes blue-red-red, etc.). These seven pieces of yarn are your seven breeding dogs.

You also have a paper towel tube–that cardboard insert thingy–with six small holes drilled in it. These holes are just big enough for you to see inside the tube.

Now use an imaginary Sharpie pen (which is all I ever have around here in real life, since my kids steal them constantly) and mark the holes with your six top priorities in breeding. Let’s say tracking ability, dark eye, tight hips, good bite, running drive, angulation. All of these are really, really good things to have in a dog, and I am all for making these predictable.

Now drop the ends of all your pieces of yarn through the paper towel tube and get ready for the magic.

Looking ONLY through the tiny holes, carefully pull one piece of yarn past the other pieces of yarn (or vice versa) until what you are seeing through the holes is exactly lined up. Through the dark eyes hole you see red-green-yellow or what have you; through the tracking hole you see blue-yellow-red, etc. In each hole you see all the identical pieces of yarn making the same pattern.

Hallelujah! You have just successfully inbred (or linebred; it’s the same thing when it comes to this experiment) a perfect breeding population according to Of Peas and Pups. No matter how you breed these seven dogs together, you will ALWAYS get a dog with dark eyes, tight hips, lots of nose and run, good angles, good teeth. Absolute predictability, absolute prepotency (prepotency basically refers to how much influence the parent generation has on the offspring generation–a numerical prediction of how much the kids will look like and act like the parents).

Unfortunately, that’s where Of Peas and Pups ends. It’s all a rosy glow of predictable production of perfect puppies with nary an outlier in the bunch.

Unfortunately, it completely forgets the rest of the yarn.

When you develop perfect homozygosity for traits, you’re developing perfect homozygosity for traits. The six–or ten, or twelve, or fifteen–you can see, the ones you’ve been trying to influence, you really can get just about perfect. And for many breeders, these are not just looks or ability. They inbreed to avoid health problems too, and they do a very good job of it. You really can develop a population completely free of, say, von Willebrands, or PRA, or other simple genetic diseases (simple meaning that the gene means the dog gets the disease, that there’s not an environmental component). You can even make a lot of headway against disorders with a major environmental trigger.

Unfortunately, even if you can manage, say, fifteen holes in your cardboard tube–and that would be an INCREDIBLE number to succeed in as a breeder–the VAST majority of the genetic code (those repeated strands of yarn) is still hidden from view.

And some of the stuff you CAN’T see, and may not in fact see for generations, would be labeled something like “resistance to parvovirus strain CCXI” or “production of tumor necrosis factor under specific conditions” or “unique myelination of nerves.” Hundreds and thousands and quite possibly millions of these traits are ALSO being made completely homozygous.

This is what makes an intensely homozygous population–your seven dogs, and in some breeds virtually the entire population of forty thousand dogs or four hundred thousand dogs–INCREDIBLY vulnerable.

Here’s how it works: Your population of predictably beautiful and birdy dogs chugs along pretty happily for a while, but then a new environmental threat or pressure comes to bear. Very often this is a disease, but it can also be a diet change (the way we feed dogs has flip-flopped in an incredible way over the last 50 years, with generations being fed almost entirely differently than the prior ones and differently from the subsequent ones) or a husbandry change (more weight, less exercise), or a vaccination change, or any number of things.

In a maximally heterozygous population, where the yarn doesn’t match up on almost any region, the dogs’ individual bodies will respond in many different ways. If the threat is a virus, some dogs will have genes that code for a protein that does a better job than the other dogs’ proteins at sticking to the viral coating and therefore coding for an antibody. So those dogs will get over the disease much faster. Other dogs will have a greater fever response, a more labile body temperature. So those dogs will spike a fever instantly and possibly kill more viral particles. And some dogs will have a sluggish reaction and very little immune response and they’ll die.

When you have a homozygous population, there’s no ability for some dogs to zig and some dogs to zag. Every single dog will respond the same way to the threat. And for some threats that’ll be a good thing, because they all survive (that’s how you breed plants resistant to certain fungi, for example). But for other threats it will be a catastrophic thing.

It is VERY well established that homozygous populations are super vulnerable to what are called plague diseases–not “the plague,” but a term that population ecologists use to refer to any disease or threat that sweeps through the entire population.

The second huge threat to very homozygous populations is that of polygenic disease.

Genetic disease is very, very rarely a simple thing. There are a few diseases that have a one gene equals one disorder formula, but this is only a tiny minority. Most diseases have a complex recipe of genes interacting with each other, with the eventual symptoms triggered by environment.

So, for example, the gene sequence for osteosarcoma might be RSTAUU, where each letter represents an entire gene (a sequence of many base pairs).

If you look across the entire population of dogs, a whole bunch might have RS, a few have TA, a very small number have RSAUU, a proportion has UU, etc. It’s pretty rare that they all occur together in one dog.

But what happens when you align all those yarn pieces, when you remove heterozygosity, is that those cancer genes get aligned too. The dogs that tended to be just UU also had iffy bird sense, so they were selected against and disappeared from the population. The dogs with just RS had light eyes, so they’re gone too. The result is a ton of dogs with RSAUU and another ton of dogs with TA.

A dog with RSAUU won’t get cancer. Neither will a dog with TA. Nobody INTENTIONALLY bred cancerous dogs. They looked like two entirely healthy populations.

But when they came together, a population with a huge proportion of dogs that will get the entire RSTAUU sequence was created. And that is something that is INCREDIBLY difficult to undo.

And we have precisely that situation in Boxers and Goldens and Flatcoats right now–such enormous cancer rates that the effective lifespan of the breeds has been cut nearly in half. Breeders are aware of the issue, appalled by the cancer rates, and are working like the dickens to reduce them, but when you have a polygenic disease it’s very difficult. You don’t know if the reason Ch. Besom’s Big Boy was cancer-free until old age was because he actually didn’t have cancer genes, or if it was that he was TA. You don’t know whether your lines have TA or RSAUU, so if you breed your cancer-free Ch. Lori’s Twinkle Toes to him you could end up with a super healthy litter or you could end up with a disaster. And even if you do end up with a healthy litter, you might wreck it all in the subsequent generation.

In other species, when you find yourself in a corner you either kill every member of your breed and start over (this is what happens in plants–you let Soybean Strain WW23, which turned out to be vulnerable to a certain insect, get plowed under and you buy WW24 from the seed company the next year) or you breed your way out by accessing completely different genetics. You take your Alpine goats that are producing an uncomfortably large proportion of skin diseases and you breed to Saanen bucks for a year, then breed those kids back to your Alpines. The ADGA (the goat version of the AKC) has a specific provision for this; as long as you use registered animals you can cross-breed and then breed back into purebred status with a letter attached to your registration number.

The AKC has no such plan or provision except under VERY specific circumstances. I applaud every breed club that has gone that route and has sought out alternate breedings when it became clear that they had bred themselves into a corner; I sincerely wish more would follow suit.

But the point is that with an almost entirely closed studbook (i.e., we can’t breed into different breeds or to unregistered dogs), we remove genes at our own great peril. We do not have any idea, and probably won’t for another fifty or a hundred years, what protective or preventive genes we lose when we move toward maximum homozygosity.

It is well worth considering that a huge proportion of all behavioral adaptations on the part of complex animals, from fish to humans, are designed to get you away from breeding with your relatives. Losing heterozygosity is a quick trip to species death.

Because we control our dogs’ breeding decisions, we can do a great deal of good, we can select away from disease, we can select for traits that maximize the dogs’ abilities to do their jobs. And we MUST do those things. But I strongly suggest that we treat a high coefficient of inbreeding with no little caution, and we move toward maximum heterozygosity wherever it is possible. For the long-term health of our breeds, far beyond next year’s sweep of the trophies, it’s something we must consider.

Inbreeding and using COI to analyze potential pairings (yet more on Pedigree Dogs Exposed)

One of the topics that Pedigree Dogs Exposed brought up was inbreeding, or the practice of breeding together close relatives in order to come up with a more predictable result than you’d get if you bred two unrelated dogs.

(people who know this already can check out here and resume close to the end, because I want to explore exactly what inbreeding is and why breeders do it)

In my family (my own background) there are closely related (first cousins or closer) women who are as short as 5’2″ and as tall as 5’11”, and from very light-boned and tiny-framed to big and broad. In Doug’s family, there are women from 5’0″ to 5’8″ and who span a similar range of frame sizes. That means that when we had female children, even though I am 5’6″ and he’s about 6’0″, we would never expect every child to grow up to be my height or even between my height and his height. It’s quite possible that I carry a bunch of genes that code for shorter height than I myself show, and it’s quite possible that I carry a bunch of genes for taller than I am. His situation is similar.

And, in fact, this is borne out in our family. We have an average to tall daughter with a strong frame, an average daughter with a narrow frame, a very short and tiny daughter who is proportional, and a baby who (so far) is tall but light.

We did not reproduce predictably when it comes to height and skeletal weight.

On the other hand, we have very little variation in our families when it comes to hair and eye color and skin color. We both come from families that are exclusively fair, with either blonde/brown or red hair, and eye color is very consistently blue. So we had absolutely no surprises when it came to the skin, eye, and hair color we produced–everybody’s blonde or red and has extremely light skin and blue eyes, and there’s no possibility for anything different. In this area, we will always reproduce very predictably.

This is, basically, just the way it works in dogs. If you breed together dogs with a wide variety of genetic expression behind them for a particular trait (this is also known as heterozygosity), you will produce dogs with a wide variety of genetic possibilities and therefore many different physical appearances.

If you breed together dogs with a narrow range of genetics behind them for a particular trait (homozygosity), you will produce dogs with a very narrow range of physical traits.

This can also work if you have just one parent who is very homozygous for traits. Most of us have a lot of different alleles that control which genes are expressed. I don’t want to get too much into junior high genetics, but if I’m Aa Bb Cc dd, and Doug is Aa Bb Cc Dd, our kids could be (AA, Aa, aa), (BB, Bb, bb), (CC, Cc, cc), (Dd or dd). Those lowercase pairs are recessive traits. If, on the other hand, I’m Aa Bb Cc dd, and Doug is AA BB CC DD, his capital letters will overwhelm all my lowercase letters and none of the possible recessive traits will be expressed. This will create a group of children who look much more alike than they would if he had a mixture of dominant and recessive alleles and so did I.

One of the most potent ways to reduce heterozygosity and reliably produce offspring that look very similar to the parents and to each other is to breed to relatives. You can immediately see how this would work–nobody’s contributing that black hair from across the ocean, or that olive skin.

And so this has become a major tool in the dog breeder’s repertroire.

Over a long period of time, you can develop an extremely reliable system for making predictable dogs. (This is not, by the way, how most breeds are formed–this is how some breeders operate within established breeds. It is important to keep this in mind.) Breeders who do this can end up with such a distinctive look to their dogs that it’s immediately apparent whose dog that is across the ring, even if you’ve never seen the dog before.

And it’s not only true that those breeders have very predictable or distinctive looks in their own dogs; because of the lack of heterozygosity their dogs are very likely to produce that look even when bred to unrelated dogs. So you can get that look by choosing one of their stud dogs to breed with your bitch, even though your bitch doesn’t look much like them at all.

An important variant on inbreeding is LINE-breeding, which is a form of inbreeding where the genes of one particular individual or a closely related individual are concentrated in the resulting puppies. For example, if I have a bitch and I really like her, but I think her great-grandfather on her mother’s side had a prettier head, I would not breed her to a relative on her father’s side, or to her own brother. I’d breed either to that actual great-grandfather or to his brother or to another dog related to him. I’d try to concentrate the genetic material of that handsome g-grandfather as much as I could, in an attempt to create puppies that look as much as possible like HIM, not like any other dogs.

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.

So why are you talking about goldfish in the title, then, you may ask.

COI is actually short for coefficient of inbreeding. The dog’s COI is a numerical expression of how many shared ancestors he or she has. For example, if you look at just the dog’s parents, the COI will be zero, because the parents are (obviously) not the same dog. But if you go back another generation, you see that the parents were half-siblings. This throws the COI up to around 15%. If the parents were full siblings, the COI is 25%. If the parents were full siblings AND the grandparents were related AND the great-grandparents were related (or the grandfather one one side was also the great-grandfather on the other side, etc.), you can quickly get up to a COI of 30-40%. At this level the puppies are quite inbred.

What often happens in dogs is that when you’re looking at two paper pedigrees, which usually list four generations, and imaginging a cross between these dogs, you see a few shared relatives but not a huge number. So you can conclude that you are not breeding closely related dogs. But when you expand the search to ten generations (from 64 dogs to 1024 dogs) you very frequently find that in fact you are breeding the equivalent of cousins. The ancestors in common were found in those prior generations. So the breeding you thought was between dissimilar dogs is not. There are several breeds that have high COIs across the board, like Australian Shepherds and Standard Poodles. The average COI in those breeds makes the typical breeding, even when very few or none of the dogs in the five-generation pedigrees match, closer than first cousins. You don’t see that until you get back to ten generations or so.

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.

OK, here’s where we come to the controversial part of my little tale.

Many dog breeders use the COI to help choose breeding partners, but they actually push toward a HIGHER COI rather than a lower one. They will seek out those individuals with high COIs because those are the ones that are going to make a more predictable puppy.

The generally accepted “formula” in show dog breeding is to breed closely (make high COIs) for the majority of breedings, bringing in an “outcross” (a lower COI) only occasionally. This is, invariably, related to me as “what my mentor told me to do” or “a respected older breeder told me to do.”

As I said, this is an incredibly potent method for making predictable looking puppies. You can get yourself a lot of champions that way.


I’ve been involved in many more species than dogs, and I can tell you that the only breeders who have the philosophy that closer breeding is preferable to outcrossing are the dog fancy and the import-bred Arabian horse fancy. The rest of every other group I’ve been involved with (cow, goat, sheep, rabbit, other horse) thinks that this is CRAZY and INSANE. They don’t even use the words like we do–it’s not an “outcross” if you breed to an unrelated sire; it’s just a normal breeding.

They breed relatives only for specific purposes and they don’t keep doing it, or they may deliberately inbreed for a couple of generations to make one inbred sire that can be used on a lot of unrelated females to create a specific result, but then they don’t keep inbreeding. The vast majority of their breeding decisions put together completely unrelated animals.

If you have no genetic heterozygosity, you have vastly reduced resistance to disease across the population (because every dog has the exact same genetic resources to use to fight disease; there won’t be some that do better than others), and you have a very real danger of ending up in a genetic corner with nowhere to go. There are about a hundred other reasons, some more or less important, but the bottom line is that there’s a reason that animals evolved behaviorally to seek out the least-related genes to pair with.

I understand the drive toward predictability in type, but we’re facing a situation in purebred dogs where so many breeders have done this for so many decades that we have a super tiny gene pool even in the common breeds. This is a situation that is instinctively understood to be unhealthy by just about everyone who is not breeding show dogs; as I said, in every production- or longevity- or health-based species (in other words, where “success” in that species means the ability for it to consistently do a job) they do not follow this strategy. The elevation of predictability–not even type, it has to be predictability in type–above other considerations is something that needs to be done with extreme caution.

It’s also very pertinent that we are under fire from welfare groups and the general public for doing this kind of inbreeding–and honestly there’s no difference in terms of genetics between linebreeding and inbreeding; those are labels we dog folk put on it to say we are inbreeding to a specific dog or set of dogs, but it doesn’t mean a lot objectively–and this is going to become a battleground.

The breeders of production species have managed to create very high-quality breeding programs without using a high COI. Showing goats or showing sheep or showing rabbits is just as demanding as showing dogs– in fact, in goats (with which I am most familar) it’s actually MORE demanding because the judges have to give critiques and because you have a linear appraisal system where the animal is compared to a mythical perfect goat. So your goat is exposed as crappy no matter how many other goats it has beaten in the show ring.

That’s an important lesson, I think. They did it, and continue to do it, by pairing animals that move toward a desired look and a desired production level, without using close breedings.
I do want to be clear on this, now that I’ve made everybody mad: COI tells you nothing about whether the two dogs are going to produce high-quality offspring. I could get a really low COI by breeding to an entirely different breed, but that doesn’t mean it’s a good move. You still have to choose a stud dog or bitch based on his or her quality and health testing and so on. And a low COI shouldn’t trump the more immediate issues of temperament or disease. COI is one more tool you use to structure a breeding program, especially a long-term breeding program, and it helps you understand how your prospective matings will or will not support your efforts and what I hope are the efforts of your breed club.

Committing to a lower COI as much as you possibly can–not to the detriment of the dogs, but as a general rule–will create a breed that is substantially more sustainable over the long term (I mean decades or centuries here, which is–I hope–an important part of how breeders are planning their breedings).
If I can say one thing about this and have it be remembered, it’s this:

There’s a story I heard years ago of a young woman who was putting in the roast for Sunday dinner. Her guests watched as she carefully cut off a portion of one end of the roast before putting it in the pan to cook. One family friend asked “Wow, that’s really interesting. Why do you do that?” She said, “My mom, who was the best cook I know, taught me to always do this.”

Fascinated, the friend called the woman’s mother. “Why do you cut the end off the roast?” She replied, “My own mother, who was a fabulous cook, always did it, and I have always thought it was important too.”

And so the friend called the elderly grandmother, related the story, and said “So what is it that makes cutting the roast end so critical?” The grandmother laughed and laughed. “My goodness!” she said. “I didn’t have a big enough roasting pan. I had to cut the end off the roast to fit it in the pan!”

The time of just following what an older breeder told us is over. Own your own decisions! You must know what you are doing and be able to explain exactly why you are making the breeding decisions you are making, and “so and so told me it worked” is not enough. We are breeding in a totally different and often overtly hostile environment and, if we are not already, we’re going to be under an incredible amount of scrutiny.

Inbreeding is a huge part of why we’re perceived as borderline animal abusers. So if you choose to inbreed (and you can’t avoid this by looking at a short pedigree; the many-generation COI is important), you need to be able to justify it based on facts and studies and in-depth knowledge of the dogs and the pedigrees, not on what someone else always did.

Or, someday, you or somebody in your breed is going to be sitting in an interview room being made to look like at best a fool and at worst a pervert. If you think I’m overreacting, go watch Pedigree Dogs Exposed.

Implications of the Kennel Club decision on the Pekingese: Pedigree Dogs Exposed



Introductory Material (links to the program and a comparison of the old and new Pekingese standards)


Part 1: The background of the decision


Part 2: How Pedigree Dogs Exposed was both factually incorrect and wrong in its conclusions


Part 3: The Pekingese in particular


Part 4: So where do we go from here?


Related Topics: Inbreeding



The implications of the Kennel Club (UK) changes to the Pekingese standard; also Pedigree Dogs Exposed. Part 1.

OK, I promised I’d get to the Pekingese and UK Kennel Club situation and here it is. I’ve been stewing for a couple of days about exactly how to communicate what I’m thinking and worried about, and I suspect this will be a very large post, so settle down and get a cup of coffee.

This can’t be told without going back a few years. Across Europe-and this is a situation very unlike the dog breeding culture in the US-there is a feeling that government is responsible for pet animal welfare to a very great extent. There is an expectation for rules-making that would be considered invasive and even unlawful here. For example, in some Scandinavian countries bitches are not allowed to care for more than eight puppies; any additional whelps must be put down. Failure to do this means the “breed wardens” will throw you out of the breed club and quite possibly you’ll be blacklisted. It’s a very interesting paradox; the acceptance of dogs as part of normal life is higher there (for example, dogs are often allowed in restaurants and shops), there is a much lower tendency to perform “routine” procedures on dogs (including spay/neuter, although there are very few unwanted litters), but there’s also a much greater interference in terms of what dogs may be owned or bred and how and when.

Into that culture came the recognition of a term that, across all the countries I can find it, is translated as something like “pain-breeding” or “torture-breeding.” Pain-breeding is the production of a weird dog, basically. It’s when you breed a dog with a very short face, very short legs, long spine, lots of coat, or any other trait that could be seen to interfere with the dog having a “normal” (we’ll get to that later) life. Pain-breeding also means any kind of pairing that could possibly result in dogs that are unhealthy. This particular clause tends to affect those dogs that have possibly deleterious recessive genes but are themselves healthy (like dogs who carry for but do not express PRA, an eye disease), or those dogs that when bred together may produce a disorder relating to color (for example, breeding two merle collies, or two harlequin Danes, or two blue Dobermans).

Germany passed the first pain-breeding legislation that I am aware of, earlier in this decade. It forbade, among many other things, breeding two harlequin Danes or two dapple Dachshunds together, and outlawed a long list of breeds perceived to be either unhealthy or prone to aggression (which was, as far as I can tell from the German breeders, part of the same philosophy-it’s not so much “they’re unsafe” as it is “it’s unfair to the dog to breed them when they have tendencies like this”). The breeds forbidden were done so under the German Animal Welfare Law, which gives an indication of the philosophy behind the decision.

You need to know those three things-that there is a focus on a “natural” dog as opposed to an “unnatural” dog, that there is a feeling that any breeding that could possibly produce an unhealthy puppy (even if that puppy would be put down at birth) should be forbidden, and that there is a greater acceptance of dog-related legislation-to understand what’s going on in the UK right now.

Coming back to the present, this year the BBC sponsored and broadcast a… well, let’s very generously call it a documentary-style program, called Pedigree Dogs Exposed. It was a total piece of schlock journalism that basically can be summed up as “Purebred dogs? Parade of mutants! Kennel club? Moronic eugenicists! Breeders? Money-grubbing builders of gingerbread houses! You know who liked dog breeding? HITLER!”

I watched it and it’s honestly laughably inaccurate, both in facts and in conclusions, but it created a groundswell of dog-show hatred (and breeder hatred, and Kennel Club hatred) especially in the UK but around the world as well. The RSPCA withdrew from Crufts (and this is me being cynical here, but I believe this was their plan all along-the RSPCA’s vet was the one who called a dog show a parade of mutants). People were doing the Internet equivalent of running around waving their hands in the air screaming. And the Kennel Club itself… well, let’s talk about that in a minute.

That program “exposed” three categories of issues in registered dogs: extreme breed traits, inherited disease, and inbreeding.

Let’s define extreme breed traits first. The program pointed out the issues they say are the result of extremes in face, legs, spine, tail, and coat. It strongly alleged that breeding for any conformational detail that took a dog away from wolf-hood was detrimental to that dog to the extent that it deviated from the wolf, and pointed out some specific examples: the brachycephalic head of the Peke, the curled tail of the Pug, the dwarfed legs and long ears of Basset Hounds, the extreme angulation of the German Shepherd Dog, the large eye of several breeds, and the ridge of the Ridgeback (which got an extra helping of hatred because some breeders put ridgeless puppies to sleep at birth).

Second, they targeted inherited disease. Here they pointed out the epilepsy that plagued a sweet Boxer and the malformed skull and mitral valve disease in Cavalier King Charles Spaniels.

Third, they made some really stunning allegations about the vague and undefined evil of inbreeding, which was said to cause horrible diseases and mental defects and infertility.

They served it all up with a big swirly topping of vets decrying deliberately breeding mutations and how terrible inbreeding is, and owners weeping over their sweet sick dogs.

Well, the Kennel Club LOST ITS BOWELS. As far as I can tell, there must have been about twenty people in a board room having a complete fit. I’m tempted to call them naïve, but maybe it really is the truth that they hadn’t ever had charges like this leveled at them. The Brits LOVE their dogs, really adore them. So maybe the Kennel Club felt that it would enjoy the cozy approval of the entire country indefinitely.

And here is where the Kennel Club made what I feel to be a completely horrible decision and perhaps one that will end up being fatal to its role in the UK. It is a move that I feel indicates a genuine emergency on the part of the purebred dog community world-wide.

Instead of responding to each of the allegations of the program and explaining where and how they were incorrect, the Kennel Club AGREED. It not only agreed, it promptly shifted blame to the individual breed clubs and accused them of cruel and inhumane breeding practices.

The breed clubs were, understandably, horrified. This is their parent club; they have always felt not that this was a boss but that the Kennel Club is the very best of what they are. The people accusing them of not caring for their dogs were once (and many are still) breeders themselves; the KC, it is felt, should have had the breeders’ side on this.

Specifically, the Kennel Club announced the following sweeping changes:

1)      Each standard (the description of the perfect purebred of that breed) would be reviewed and changed by fiat as necessary. If you’re not in purebred dogs, let me just tell you what an incredible assumption of power this is. Breed standards do change, but they do so extremely slowly and the major impetus behind each change is the breed club (for example, the Pekingese Club), not the Kennel Club. The breed club typically has a Standards Committee and spends literally decades considering whether the breed needs even the most minute changes to the standard. I’ve been in on months of deep and passionate arguments about whether a dog’s elbow should mark half the distance to the ground from the shoulder or if it should be an inch above that. Some people believe so much in the traditional description of a breed that they will talk longingly of the glories of, say, the 1971 standard, which was probably published when they were ten years old and which varies from the 1993 standard by half of one paragraph. The Kennel Club’s normal role in changing a breed standard is to provide input on the correct format of the proposed change or changes, to make sure that the wording will be clear to the judges, to suggest clarification, etc. For it to seize control of standards and change them without breeder input is shocking and unprecedented.

2)      The standards would be changed with one goal: to reflect an emphasis on “health.” Now let me assure you that they don’t actually mean health, or longevity. They mean “less exaggeration.” The Kennel Club has totally bought, or is pandering to, the notion that deviation from the wolf equals detriment to the dog, with the extent of the deviation indicating the extent of the detriment. This is TOTALLY INSANE, as I will try to discuss later, but they bought it. And so the Kennel Club has promised to focus on the exact issues that Pedigree Dogs Exposed insisted were problematic-short faces, short legs, curled tails, heavy coat, long spines, long ears, and angulation.

3)      The Kennel Club implemented a Code of Ethics for all breeders and forced each club to adopt it. This, again, is a power it has never before assumed.

A  Code of Ethics is sort of like the standard for breeders. It describes what it means to be a good breeder of that breed, and is a valuable tool for prospective owners and also for prospective breeders. Most, if not all, breeds have a COE, but aside from some standard statements about humane breeding they vary considerably between breeds. The COE reflects the best practices for that particular breed or responds to a situation the breeders perceive to be an issue for that breed and that breed alone.

So, for example, in the US the Pembroke Welsh Corgi COE mandates that puppies not be sold before the age of ten weeks. The Cardigan COE has seven weeks, but forbids the retouching of show or informational photographs. I don’t even pretend to know what situation led those particular elements to be added to the COE of the breeds, but there they are.

The fact that the Kennel Club handed down a COE that must be adopted by all breed clubs was, again, an implied accusation that the breed clubs could not be trusted to make their own decisions or weigh for themselves which practices define a good breeder.

4)      The Kennel Club is currently seeking legislative powers that will make it law to belong to the club’s Accredited Breeder Scheme if you want to legally sell puppies in the UK.

(Continue here to Part 2.)