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Is COI an essential tool or just a fad?

5/22/2022

 
By Carol Beuchat PhD
The coefficient of inbreeding was derived by Sewell Wright back in the 1920s to provide animal breeders a way to quantitatively assess relatedness of animals in lineages with complex pedigrees. It's easy to estimate relatedness of individuals from a few pedigree generations, but as the pedigree gets deeper, and inbreeding and crossings among lines get more complex, estimating relatedness of pairs of individuals becomes an overwhelming task.

Why was estimating relatedness important? Back in the day, breeders understood the general effects of parental relatedness on quality of offspring. They knew that a bit of inbreeding increased the uniformity, predictability, and quality of many traits in offspring. But they also found that too much inbreeding had negative effects, a phenomenon called "inbreeding depression." Starting with a population of outbred animals, Wright summarized the dual consequences of inbreeding here (Wright 1922):
"First, [there is] a decline in all elements of vigor, as weight, fertility, vitality, etc., and second, an increase in uniformity within the inbred stock, correlated with which is an increase in prepotency in outside crosses... The best explanation of the decrease in vigor is dependent on the view that Mendelian factors unfavorable to vigor in any respect are more frequently recessive than dominant, a situation which is the logical consequence of the two propositions that mutations are more likely to injure than improve the complex adjustments within an organzism and that injurious dominant mutations will be relatively promptly weeded out, leaving the recessive ones to accumulate, especially if they happen to be linked with favorable dominant factors.  On this view, it may be readily shown that the decrease in vigor in starting inbreeding in a previously random-bred stock should be directly proportional to the increase in the percentage of homozygosity... As for the other effects of inbreeding, fixation of characters and increased prepotency, these are of course in direct proportion to the percentage of homozygosis.  Thus, if we can calculate the percentage of homozygosis which would follow on the average from a given system of mating, we can at once form the most natural coefficient of inbreeding.”
Wright is saying that deleterious mutations that are dominant will show their effects and can be weeded out, but recessive mutations that have no effect unless homozygous will tend to accumulate in the genome over time. Consequently, crossing related animals runs the risk of producing offspring that are homozygous for previously silent recessive mutations, with deleterious consequences that can range from an obvious functional defect to subtle changes in health, vitality, longevity, and so on. Therefore, breeders in Wright's time wanted to be able to figure out the level of inbreeding so they could balance the benefits with the risks when striving to producce the best quality animals.

Wright realized that because both the positive and negative effects come from alleles on individual loci, changes in the fraction of loci that are homozygous would have a direct and proportional effect on the traits that are improved as well as those that are detrimental. This allowed breeders to identify the "sweet spot" in COI where their animals would have the highest value because of the best tradeoff between benefit and detriment.
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Wright's development of the coefficient of inbreeding revolutionized animal breeding because it provided a quantitative estimate of inbreeding based on an understanding of probability in inheritance of alleles. His expression of this has arguably been the most powerful tool in the box for breeders over the last century, and it remains just as important now as it was then because it is grounded on the fundamental processe of independent inheritance of alleles. In many populations of wild and captive animals (and plants, too!), the coefficient of inbreeding, and its related statistic, the kinship coefficient, remains the primary means of genetic management.
So why is it that I hear breeders declaring that "the inbreeding coefficient is "just a tool" or a "fad", or a crude, dusty relic of the olden days when breeders only used paper pedigrees for breeding? It is claimed to be "inaccurate", "pretty much worthless", and not useful now that we can estimate genomic inbreeding from DNA analysis. If this was true, why would today's foremost scientists in the fields of population genetics and animal breeding management still be using it? 
Well, I think a lot of breeders say these things because they heard somebody else say them. This is the "folklore" model of information development, where the loudest voices can produce "information" that is accepted by the masses because nobody does the fact check. People parrot these memes because it's what everybody else says, and they don't understand the biology enough to questions anything. The consequence is that you can't make the best breeding decisions working from bad information, and after all the work and expense that goes into breeding, nobody wants to do that! 
In truth, we will continue to use the coefficient of inbreeding as long as we continue to breed animals and plants, which will be as long as we inhabit this earth. Here are a few reasons why, and these are also the ways you should be using it now.
First, the inbreeding coefficient can be used to reconstruct the genetic history of a population of animals. Dr Pieter Oliehoek used it in his analysis of the population genetics of the Icelandic Sheepdog to document the loss of genetic diversity over time, as reflected in the increase in average level of inbreeding in the population.

Oliehoek also used a related statistic, the kinship coefficient, to reveal how breeding strategy in the population had changed over time. The kinship coefficient measures the degree of relatedness (in terms of genetic similarity) between two individuals. The kinship coefficient is also equal to the inbreeding coefficient of offspring produced by a pair of animals. In other words, the inbreeding coefficient of an animal is the kinship coefficient of its parents. When Oliehoek plotted both the inbreeding coefficient (black symbols and line on the graph below) and kinship coefficient (red symbols and line) on the same graph as probabilities (i.e., values between 0 and 1.0), he showed that in the early history of the breed, there was preferential avoidance inbreeding that is revealed because average inbreeding was less than average kinship in the population (the black line is lower than the red line); that is, breeders chose to pair individuals that were less closely related than average in the population. This was the case until the early 1980s, when these lines flipped, with the average inbreeding increasing faster than average kinship, reflecting a preference by breeders for closer inbreeding, even when pairs were available that would produce lower levels of inbreeding.
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Oliehoek also used the kinship coefficient in a very clever way, to reveal the decline in the size of the gene pool over time. In the chart below, he used the relatedness of each animal in the population with every other animal in pairwise comparisons to compute "mean kinship" (Nmk), which is a measure of the size of the gene pool. This is expressed in terms of how many founder dogs would result in a gene pool of the same size, something called the "founder genome equivalents. This graph below shows that the population started with the equivalent of about 20 unrelated founder dogs in about 1955, but by 1975, only 15 years later, the size of the gene pool had dropped to the equivalent of only about three dogs, and it continued to decline in subsequent decades. By the end of the 1990s, breeders had the genetic diversity of only 2 dogs to work with. Again, this information is derived from calculation of the genetic relatedness among the dogs in the population from the kinship coefficients, which estimate the predicted COI that would result from a particular mating. 
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The brown squares along the x-axis of the graph above represent the importation of new dogs into the population. Breeders assumed from scrutinizing pedigrees that these dogs were relatively unrelated to their breeding population and would therefore restore some lost genetic diversity and reduce the level of inbreeding. But Oliehoek once again used the kinship data to reveal that the population of the breed had clusters of related dogs, and that unfortunately, the imported animals were genetically part of the main cluster so did nothing to improve genetic diversity. The chart Oliehoek produced below showed where relatively less-related dogs could be found in other clusters, and it also showed that some of these other clusters were perilously small in size and at risk of extinction. Breeders could use this information to make better selections of dogs to import, and to also make sure that lines with small numbers of dogs were not accidently lost.
We can see that the coefficient of inbreeding and the related statistic, the kinship coefficient, can be valuable tools in providing breeders with information that can be used for breeding decisions as well as population management. But the inbreeding coefficient has another, extremely useful role to play, this one in the prevention of genetic disorders and inbreeding depression. 
The inbreeding coefficient quantifies the probability of an animal inheriting two copies of the same allele from a shared ancestor. This is also the fraction of all loci that are expected to be homozygous. We can put this information to use to reduce the risk of genetic disorders in offspring.  
We know that most genetic disorders in dogs are caused by autosomal recessive mutations, with estimates ranging from about 60% to 80%. So, for these health issues, the risk of producing a problem in a puppy is equal to the probability of that puppy inheriting two copies of the same mutation, which is exactly what the coefficient of inbreeding tells us.

So, if the inbreeding coefficient is 25%, the equivalent of a pairing of littermates, the risk of producing a genetic disorder caused by a recessive mutation is also 25%. Similarly, if the COI is 40%, there is a 40% chance of a puppy inheriting two copies of the same mutation. Likewise, a COI of 10% puts the risk of producing a genetic disorder from a recessive mutation at 10%. When recessive mutations account for such a large fraction of all genetic disorders in dogs, the benefits of being able to reduce or even prevent them is very significant.

Note that this also means that if the inbreeding coefficient predicted is much below 25%, there would be little benefit from doing DNA tests. 

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Remember that there is another deleterious effect of inbreeding apart from causing genetic disease from recessive mutations, and that is inbreeding depression, which is a general decline in the traits for "fitness" - things like lifespan, fertility, and what breeders used to call "vigor" or "vitality". These are not caused by a mutation per se, but by the loss of advantageous alleles or combinations of alleles at particular loci. For instance, there is something called "heterozygote advantage", in which the heterozygous genotype is more beneficial than either homozygous state (i.e., Aa is better than either AA or aa). You lose these beneficial allele combinations when inbreeding, and even though the effects can be are subtle, they can impact the quality of life of the animal in important ways.
These properties and uses of the coefficient of inbreeding are why it remains an essential tool in the savvy breeder's kit today. Even in the face of new molecular technologies, it will still be around for the long term because it can provide information we can't get any other way. Inbreeding can now be estimated from DNA genotyping data, avoiding the limitations of using incomplete or potentially erroneous pedigree data. But for genomic inbreeding, you must have a DNA sample from the dog of interest, which might not be possible if the dog lives far away or no longer alive. But a well-tended pedigree database will provide information for any dog in the breed's history, limited only by the care taken when curating the pedigree database.
The Coefficient of Inbreeding has been around for a long time, and it is no less useful today than when it was first described by Wright a century ago. Genomics can now provide us with lots of information that was just a dream only a few years ago, and it's fair to say that we are in the midst of a new era of what can fairly be called "precision breeding" . But as long as breeders continue to use pedigrees when making their breeding plans, the inbreeding and kinship coefficients will continue to be used to estimate relatedness, predict litter inbreeding, and balance the benefits of prepotency and consistency with the risk of genetic disease and inbreeding depression. 


REFERENCES

Oliehoek, PA, P Bijma, & A van der Meijden.  2009.  History and structure of the closed pedigreed population of Icelandic Sheepdogs.  (pdf)

Wright S, 1922.  Coefficients of inbreeding and relationship.  Am Nat 56: 330-338. (pdf)

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The elephant in the room? Incest breeding.

5/20/2022

 
By Carol Beuchat PhD
There seems to be a more concerted push recently to highlight the virtues of purebred dogs in the face of legal actions in Norway, new rules for showing in Germany, political advocacy in Australia about breeding, and more. Breeders are rightfully alarmed about this, and there is much discussion in many forums online about how to respond. Invariably, the consensus is that "we need to fight!" Unfortunately, fighting back is not going to make this go away. Here's why.
The FCI, and most breeders, are missing the foremost reason why purebred dogs get bad press and have such a bad public perception. Inbreeding. To the lay person, it's incest. In fact, it should be to dog breeders as well. The average person knows that incest is bad, that it produces genetic problems, and that purebred dogs are inbred. They are not wrong. 
​
I have posted voluminous information over the last 10 years about the truly breathtaking levels of inbreeding in dogs, inbreeding far in excess of what is needed for consistency and type. The ordinary levels in dogs are way beyond what is tolerated by most domestic animal breeders, who work hard to keep inbreeding below 10% and are concerned about every additional point of inbreeding above 5%. Why? Because inbreeding reduces every aspect of animal health, production, and performance that they care about, and we have known this for more than 100 years. Wright's coefficient of inbreeding was developed specifically to allow livestock breeders to determine inbreeding even in complicated pedigrees, because the detrimental effects were well known. Commercial animal breeders manage inbreeding carefully because it affects the quality of their animals, and that affects their profit.
The public doesn't care if their dog is registered. They don't care how much work and expense goes into breeding. Most don't even care if it's "purebred." And what does "purposefully" mean??? Tested - for what?  Most people just want a dog to love. They don't want a dog that will cost them an arm and a leg in vet bills then die in its prime. Or before. 


I can see how this FCI video will push the buttons of breeders, touching on favorite memes, but to me it just seems odd and way off the mark.
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You can watch the video HERE.
Kennel club PR isn't going to change a thing, because it doesn't address the reason the public has such a negative perception of purebred dogs. People aren't against purebred dogs. They aren't against purebred dog breeders. They are against incest breeding because it produces unhealthy animals. This is not the ARs talking; this is the average, non-dog-centric person on the street that wants a healthy dog for their family. They just want a dog to love, to be a companion, to be a member of the family.
The common response to criticism about health - and of course I expect it here, again - is that all those unhealthy dogs are coming from backyard breeders and puppy mills. No doubt there are badly bred dogs produced by the unscrupulous. But those dogs are not from a different gene pool than the population of "healthy" dogs.
In fact, like the livestock breeders, puppy mills focus on puppy production and, for that, inbreeding represents a cost they want to avoid. I haven't seen data comparing puppy mill dogs to those from the fancy, but I would be shocked if they had higher inbreeding. At the very least, puppy mills have been selecting strongly for dogs that get pregnant easily without hormone testing and reproductive "assistance", produce large litters without fuss and veterinary intervention, that care for their puppies with minimal assistance, that have adequate milk - in short, the goal is to select for dogs that will produce puppies that at least make it to the consumer. There might be a long list of other health problems, but the puppy mills are selecting for production of puppies that survive past weaning or they would be out of business. If you want to argue that it's the "poorly bred" dogs that are skewing the research and public perception, you need to find some data to prove it, because it doesn't seem very likely to be true. 
​
You will get the PR 100% wrong if it come from within the show dog breeder bubble. Step outside and go talk to the parents sitting at the soccer game. Ask the folks at the dog park why they don't have a purebred dog. Take a poll in some of the Facebook groups that are just about loving and living with dogs. People will not tell you that they're concerned about the registration papers or appreciation of the hard work of the breeder. They're worried about health. They're worried about inbreeding.
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The heart problems of the Doberman are well documented. I first wrote about them in 2016, and again with responses to that post shortly after,  as well as twice in 2017 (here and here). Inbreeding in Dobermans is off the charts (see the figure at the bottom). There's lots of research, testing, and scrutinizing of pedigrees, with no remedy in sight, as well as a huge effort to collect DNA which has apparently produced no information that is useful to breeders. I am not aware of any program that proposes to tackle the issue of inbreeding in Dobermans, without which this the breed is surely doomed. Will nobody save this breed?
By the same token, I often read comments like "I'll never understand why people want doodles when they could just have a poodle." No, you probably won't, from within the world of the dog fancy. You need to go ask the people why they got a doodle. The ones I talk to tell me the dogs are really cute, smart, fun, etc - as are most poodles, though. So why Doodles? Because the poodles they see in pictures look like a dog that - to their eyes- is not fun, not cute, not something that they want to groom, a dog that looks so elitist or stuffy. Not my words. Go ask them yourselves. It's a pity, because Poodles are wonderful dogs, but it's the eye and heart that chooses and the image is not what people are looking for. They want a dog to love, and they're willing to pay a pretty penny for it, so appreciate how they value this animal. Why don't purebred dogs fetch similar prices? It's simple. The things most highly valued by breeders are not the things dog owners are looking for. 

And while we're on the topic of Doodles. The Doodle bashing has to stop. It's nasty, cruel, and looks to the average person like elitism and bigotry. And it is. Is it going to convince anybody to get a purebred dog instead of a doodle? Of course not. Rather, it reinforces the public's opinion of purebred dog breeders as condescending and only interested in looks and show ribbons. Most people are aware that mixed breed dogs have better health and live longer because they are not highly inbred. The average person is horrified to learn that dogs are bred together that are as closely related as full siblings, yet that is common, if not the rule, in many, many breeds. The rebuttals to this from the fancy get the science wrong, and most people don't buy it. (Frequently-heard claims that purebred dogs "are just as healthy" as mixed breed dogs are not supported by the data, and indeed, I'm tired of posting the links to those sources over and over. If you want to dispute the science, go look up the papers.)


Breeders will not change the public's perception of purebred dogs as inbred and unhealthy while denying there's a problem and refusing to fix it. Sure, there are some other serious issues that need to be addressed, not the least of which is the explosion in brachycephalic breeds that wear their health problem for all to see everywhere they go. Breeders are going to have to fix this, like it or not. But you can't fix the ANY health problems if the gene pool lacks the genetic variation necessary to build a healthy dog, and all the dogs are so genetically related that they represent the equivalent of multiple consecutive generations of full-sib crosses.

I've been working with dog breeders to improve the health of purebred dogs through education, consulting and social media, and the provision of tools that can help breeders make better decisions about mate selection. Yet predictably, here we are, facing legislation to force breeders to address physical and genetic health issues, while breeders avoid addressing the elephant in the room that, ultimately, is the cause of all the problems - inbreeding. The kennel clubs and breeders are trying to fix problems without addressing the cause, and they will continue to fail. You simply cannot produce healthy dogs while engaging in unrestricted inbreeding. It can't be done.

Take a step out of the dog fancy bubble. Listen to the people in the real world. The parents at a school function. Your hairdresser. Somebody at the dog park. Your tennis partner. Get outside the bubble. People don't need to be "educated" about what you do; they don't need PR that pushes some value to registration and applauds those hard-working breeders. People really don't care about any of it. They want healthy dogs. That's all. If the purebred dog breeders are not producing them, they will go elsewhere.

Below, the most recent data documenting inbreeding in purebred dogs (from the Bannasch lab at UC Davis). The green line (0.0625) represents the inbreeding produced by a mating of first cousins, yellow (0.125) is mating of half-siblings,  and red (0.25) represents a full-sib cross (all of these assume the parents are not inbred). The black line is the inbreeding level of Cavalier King Charles Spaniels (about 40%).  
​ 
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REFERENCES

Bannasch et al 2021. The effect of inbreeding, body size and morphology on health in dog breeds. Canine Medicine and Genetics 8:12. ​https://doi.org/10.1186/s40575-021-00111-4.

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Is the Pug a "typical" dog?

5/19/2022

 
By Carol Beuchat PhD
There is a paper about the health of Pugs just pubished by the group focusing on canine health at The Royal Veterinary College in the UK (O'Neill et al 2022). They report that Pugs are less likely than other dogs to have several disorders including lipomas and heart murmurs, but they have a higher incidence of many health other issues.

It's hard to get anything out of a table of numbers, so I have produced a chart summarizing the data in their Table 2, plotting the percentage of dogs affected for each disorder, ranked by prevalence in Pugs.  (Note that they applied several statistical treatments to adjust for effects of age, weight, spay/neuter status, etc.)
​
It seems unlikely that these results reflect an unhealthy population of dogs produced by puppy mills and back yard breeders, vs the mainstream breeders in the dog fancy, because a number of these health issues result from traits stipulated in the breed standard (e.g., shortened muzzle, skin folds), but the data aren't there to support this assumption.
  
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REFERENCES

O'Neill, J Sahota, DC Brodbelt, DB Church,, RMA Packer, & C Pegram. 2022. Health of Pug dogs in the UK: disorder predispositions and protections. Canine Medicine and Genetics 9:4. https://doi.org/10.1186/s40575-022-00117-6
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