5/22/2022  Is COI an essential tool or just a fad?  
   5/20,2022  The elephant in the room? Incest breeding.
  5/19/2022  Is the Pug a "typical" dog? 
​  4/10/2022 Breeding is managed evolution
​  3/22/2022  Puppies from a breed cross will have the health problems of both breeds: T or F?
  3/20/2022  Do you know what you need to save your breed?
    3/4/2022  The genetic status of the Cavalier King Charles Spaniel, part 1: Inbreeding
  2/22/2022  The "catastrophe" of cross-breeding: meet the Borgis
  2/20/2022  We need a Mayo Clinic for dogs
​  2/10/2022  Cavaliers are in trouble
    2/5/2022  Hello breeders, this is Science
    2/3/2022  The Norway breeding ban: what does the law say?
    2/1/2022  Norway bans the breeding of Bulldogs and Cavaliers. Now what?
11/27/2021  Finally...a summary of canine coat color genetics
  10/3/2021  The easy way to improve hips and elbows
12/29/2020  How hips form and Wolff's Law
12/27/2020  The basics of hip dysplasia in dogs
    1/3/2020  Do your puppies have enough traction in the whelping box÷
  8/23/2019  Why do mixed breed dogs have so many mutations?
  8/15/2019  About pithy statements vs knowledge
    7/9/2019  Let's kill the breeder myths!
    7/5/2019  What is "heritability" and why do you need to know?
  6/17/2019  Facts vs fear mongering
  4/29/2019  Is health problem X in my breed caused by inbreeding and/or loss of genetic diversity?
  4/19/2019  No, we have NOT found the mutation that causes breathing problems in brachycephalic dogs
  4/21/2019  An update on hip dysplasia in dogs
​  4/20/2019  Addison's Disease and those doggone DLAs
​  3/26/2019  Genetic rescue and rehabilitation: I. Restoring genetic diversity of a breed
  3/12/2019  The key requirement for preservation breeding
  2/28/2019  The genetics of canine behavior goes molecular
  2/14/2019  The messy science of assessing working ability in dogs
    2/5/2019  A new ICB course that will use the DNA data from YOUR dog!
  1/20/2019  How to breed dogs that are better than their parents: the genetics of continuous traits    
    1/7/2019  The right - and wrong - way to use DNA tests
​    1/6/2019  Are breeding restrictions putting your breed at risk?
12/31/2018  More on "Simple strategies to reduce genetic disorders in dogs"
12/29/2018  Simple strategies to reduce genetic disorders in dogs
12/24/2018  Celebrating the preservation breeder!
11/27/2018  On preserving the purebred dog.
11/23/2018  Is the Ky allele in Wirehaired Pointing Griffons evidence of cross-breeding?
    9/7/2018  Cool tricks with Kinship Coefficients, part 4: How closely related are the dogs in my breed?"
    9/6/2018  Cool tricks with Kinship Coefficients, part 3: "How can I manage a disease without a DNA test?"
    9/4/2018  Cool tricks with Kinship Coefficients, part 2: "Should I breed this dog?"
    9/4/2018  Cool tricks with Kinship Coefficients, part 1: "Is this dog really an outcross?"
  8/22/2018  The easy way to understand inheritance of recessive alleles
  8/10/2018  The amazing secrets hiding in your pedigree database
  7/21/2018  We can reduce the risk of hip dysplasia NOW!
  7/12/2018  Is BetterBred better?
    7/7/2018  Assessing genetic diversity and relatedness in dogs using DNA
  6/30/2018  Using genomics to manage genetic disease. You don't need to find the genes
  6/28/2018  How much does outcrossing improve genetic diversity?
  6/26/2018  Are you improving genetic diversity, or just pushing the peas around?
​  6/25/2018  NEW: ICB Genetic Management Workshops
  6/21/2018  A DNA Primer for Dog Breeders. Genetic Diversity: Inbreeding (Fis)
  6/21/2018  A DNA Primer for Dog Breeders. Genetic Diversity: Inbreeding (ROH)
  6/21/2018  A DNA Primer for Dog Breeders. Genetic Diversity: Heterozygosity
  6/21/2018  A DNA Primer for Dog Breeders. ICB Breeder Tool Quick Start Guide
​  6/21/2018  A DNA Primer for Dog Breeders (You have your dog's DNA data. Now what?)
  6/17/2018  No pedigree? No problem!
  5/31/2018  A key innovation in dogs: diet
​    5/1/2018  The lesson(s) from SOD1and degenerative myelopathy
10/27/2017  Update on Newfoundlands
10/26/2017  Please don't ruin the Newfoundland
  8/26/2017  The amazing dog nose: can you smell me now?
​  8/24/2017  The complexity of cancer
  8/12/2017  Are preservation breeders preserving the Doberman? (No.)
    8/5/2017  Hip laxity and the risk of degenerative joint disease
    8/2/2017  Making better decisions about hip and elbow dysplasia: the era of genomics is here
  4/29/2017  New insights into the development of dog breeds
  4/27/2017  The genetic status of the Bernese Mountain Dog
    4/3/2017  How to win The Health Test Game
  3/12/2017  An update on the genetic status of the Doberman Pinscher
    3/9/2017  Lessons from wolves
​    3/6/2017  Why "vulnerable breeds" are vulnerable
​    3/3/2017  Inbreeding and the immune system: unintended consequences
​    3/1/2017  The questions PUPscan won't answer. Part 2: The answers
  2/28/2017  The questions PUPscan won't answer. Part 1
    2/5/2017  Latest OFA statistics for hip dysplasia (Dec 2016)
​    2/2/2017  Why didn't Antarctic sled dogs have hip dysplasia?
  1/23/2017  Your handy DNA testing crib sheet
​  1/18/2017  Rescuing the Norwegian Lundehund: an update from Milo
    1/3/2017  Comparing levels of inbreeding in dogs and horses
12/26/2016  Inbreeding of purebred dogs determined from DNA
​12/15/2016  NEW: ICB Genetic Diversity Certification
  12/9/2016  Why we need a more wholistic approach to managing canine genetic disorders
  12/7/2016  A simple new tool for genetic disease management
​  12/4/2016  The ICB Breeder Tool: Overview 
11/26/2016  Dog breeding in the era of genomic selection
11/23/2016  The new ICB Genomic Breeding Tool: the Genomic Relationship Coefficient
  9/18/2016  How to develop effective strategies for the genetic management of your breed
    9/2/2016  Preventing transmission of infectious disease at dog shows and sporting events
  8/31/2016  Gone too soon? Enough already.
  8/27/2016  Hip dysplaysia facts, fallacies, and fairy tales
​  8/16/2016  Why you should care about effective population size
  8/14/2016  The world's oldest cancer...in dogs 
    8/7/2016  Introducing a new course: The Biology of Dogs
  7/29/2016  Bulldog breeders: a call to action
​  7/23/2016  Try these breeding games!
    7/4/2016  Genes and the amazing mind of the dog
    7/2/2016  A game-changer for breeders: the ICB Breeder Tool
  6/30/2016  Understanding the heritability of behavior in dogs
  6/24/2016  Certificate of Completion: Genetics of Behavior & Performance course
    6/5/2016  Are we watching the extinction of a breed? (part 2)
    6/4/2016  Are we watching the extinction of a breed?
  4/15/2016  A broader view of extinction risk of dog breeds in the UK
    4/2/2016  A call for preservation breeding
​  3/29/2016  Twenty key elements of a successful breeding program
  3/28/2016  Breeds with the BEST & WORST genetic diversity 
  3/25/2016  What are we going to do about Terriers?
  3/20/2016  Evaluating the genetic status of a breed using both pedigrees and DNA
  3/15/2016  Reprise: The Pox of Popular Sires
​  3/13/2016  That purebred vs mixed breed thing again
    2/7/2016  Do you know what you don't know?
​  1/31/2016  Do you REALLY need to take a genetics course?
  1/27/2016  Three key strategies to reduce genetic disorders in dogs
  1/17/2016  Is it Nurture or Nature?
    1/2/2016  Managing risk factors for hip dysplasia
​12/23/2015  How do hips become dysplastic?
​12/21/2015  Reliability of DNA tests for inherited diseases in dogs
12/16/2015  Virtual tours of the canine hip and pelvis
12/11/2015  The 10 most important things to know about canine hip dysplasia
  11/4/2015  Coming soon: Course Certifications!
  11/2/2015  Brachycephaly: it's more than just the pretty face
10/24/2015  The poop about dog diets
​10/12/2015  Is (raw) diet the problem?
10/10/2015  Do dogs have more cancer than other mammals? 
  9/29/2015  Myths and mysteries about hip dysplasia  
  9/21/2015  Genetic status of purebred dogs in the UK
  9/16/2015  Bigger puppies develop hip dysplasia
  9/14/2015  The Mongolian Bankhar Dog Project
    9/5/2015  Citizen Scientists: Let's do something about hip dysplasia!
    9/1/2015  Major 2015 epilepsy consensus report
  8/26/2015  Genetics, behavior, and puppy temperament testing
  8/24/2015  The problem with the immune system: if you break it, it's yours  
  8/22/2015  Managing genetic disorders: "Just eliminate the bad gene"
    8/9/2015  Is the dam more important than the sire?
    7/8/2015  Decoding the genetics of behavior in dogs
  6/23/2015  Looking for early pedigree data?
  6/14/2015  For genetic improvement, it's the mix that matters
  6/12/2015  The relationship between inbreeding and genetic disease
    6/9/2015  Putting dogs to work for conservation
    6/4/2015  COI FAQs: Understanding the Coefficient of Inbreeding
    6/2/2015  Solving the problem of genetic disorders in dogs
  5/14/2015  Visualizing inbreeding on the chromosome  
  4/30/2015  The trouble with Terriers
  4/29/2015  Vulnerable breeds: how small is too small?
    4/1/2015  A bright future for purebred dogs
  3/29/2015  Health of purebred vs mixed breed dogs: the actual data
  3/27/2015  Finding genes without DNA
  3/26/2015  Tracing the paths of drifting genes
  3/24/2015  If knowledge is power, know every puppy
  3/19/2015  Lush on linebreeding
  3/12/2015  Why all the fuss about inbreeding? (Or "Why are there so many genetic disorders in dogs?")    
    3/7/2015  What does "health tested" really mean?
    1/9/2015  The history of purebred dogs in the UK
    1/5/2015  Genetic test for renal dysplasia (Caution advised)
    1/2/2015  A better way to pick 'em: using EBVs to reduce genetic disorders in dogs
    1/1/2015  Estimating the breeding value of a dog
12/31/2014  Why do dogs get cancer?
12/28/2014  Cryptorchidism is complicated
12/26/2014  Silent secrets in old dog bones
12/22/2014  The myth of hybrid vigor in dogs...is a myth
12/17/2014  Hitting the bottle: the genetics of boom and bust
  12/4/2014  More on tending the genetic pantry
  12/1/2014  Using inbreeding to manage inbreeding
11/25/2014  Why dogs are sloppy drinkers (and cats aren't)
11/21/2014  The complexity of coat color
11/18/2014  Epilepsy incidence and mortality in 35 dog breeds
  11/9/2014  Reducing genetic risk
  11/7/2014  Take the breeder quiz!
  11/6/2014  Dealing with those pesky mutations
10/31/2014  It's not always as simple as dominant and recessive
  11/9/2014  The fiction of "knowing your lines"
10/24/2014  Is your breed drifting?
10/23/2014  Who's tending your genetic pantry?
10/15/2014  How breeding the best to the best can be worse
10/10/2014  When Should You Spay or Neuter Your Puppy?
  10/3/2014  Genetic disorders in dogs: breaking the machinery of life
  9/25/2014  Get Started Using Estimated Breeding Values (EBVs)
  9/19/2014  The Costs and Benefits of Inbreeding
  8/27/2014  A bit of sheepish fun
  8/20/2014  How many generations of pedigree data should you use to estimate inbreeding?
  7/23/2014  Me, jealous?  Never!  But my dog, on the other hand...
  7/20/2014  Population Size & Inbreeding
  7/19/2014  Avoiding inherited genetic diseases in dogs
  6/18/2014  Wright’s Coefficient of Inbreeding
    6/5/2014  Why DNA tests won't make dogs healthier
    6/1/2014  Eliminating genetic disorders in dogs - too little, too late?
    5/2/2014  Better hips and elbows?  Maybe.
    5/1/2014  Cancer Surprises
  2/21/2014  Genetic Management of Dog Breed Populations
    2/2/2014  What Does Population Genetics Have To Do With Breeding Dogs?
  12/5/2013  The Pox of Popular Sires
  10/5/2013  A bit more about Poodles
  9/24/2013  An open letter to the Canadian Poodle clubs and others that love the breed
  7/23/2013  Why do dogs have so many genetic disorders?
  7/19/2013  Primary lens luxation is WIDESPREAD among dog breeds - are you testing?
  7/18/2013  Inherited myopathy in Labradors is found worldwide - the legacy of a popular sire
    7/2/2013  Finally, a scientific journal about Dogs!
    3/9/2013  How molecular genetics will change dog breeding
    7/6/2012  Locating the genes for hip dysplasia in dogs (Psssst! Look in the kibble bag)
  4/19/2012  Population genetics suggests dire straits for Tollers and Heelers

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):

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.

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. 

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.

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)

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. 
​

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.

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.
  

  

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

Wikipedia has a decent definition of evolution, as "change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction."

The key point here is that "heritable characteristics" are a consequence of the expression of genes. If the genes change, the characteristics will change. In wild animal populations, genes that produce healthy, functional animals are passed to the next generation of offspring. Genes that create deficits of some sort result in offspring that are not as successful and those animals and their genes are eventually eliminated.

For characteristics to change, the genes must change. Likewise, if the genes change, the characteristics must change. Natural selection is this process as it occurs in animal populations, and changes in the characcteristics of those populations over time are the result of changes in the gene pool, the process we call evolution.

​Breeding domestic animals is all about managing evolution, in that the purpose is to create individuals that will have the genes that produce the desired characteristics.

This is accomplished in domestic animals the same way it is in nature, by preferentially breeding the animals with the favored characteristrics and therefore, the favored genes. Once the animals have the preferred traits, the process changes from guided change to protecting the status quo, i.e.,  freezing those traits in the animals by preventing changes in their genes. If you can prevent the genes in the animals from changing over the generations, the phenotype - both what you can see and what you can't - should also stay the same. 

In domestic animals, this must be accomplished by the breeders. A successful breeder will be able to produce generation after generation of animals with the desirable phenotype, which must include both the visible traits as well as the ones you can't see or perhaps even measure. The latter will include the inner workings of the dog, which are complex functionally and genetically. ​

Selection for visible traits is relatively easy because, well, you can see them. Selection for things you can't see, or that are not easy or convenient to measure or evaluate, is lots harder. Here's the trick: how can you select for a trait you aren't able to evaluate?

The problem should be obvious. Say you have a population of healthy dogs with great type and health, and you want them to stay that way in subsequent generations. How could you do this? Well, keeping the genes for type isn't so hard. Remember, most of the critical genes for type are fixed (i.e., homozygous and the same in every dog) early in the development of a breed, and you can maintain them by selection based on physical inspection. But for all the other "invisible" traits (e.g., physiology), you need to be selecting for "invisible" genes, because as we have seen, to have the characteristics, you must also have the genes. Right. We get that. But again, how do you do this?

Everybody should be able to see the problem. To breed sustainably, you need to start with dogs that have the genes for your perfect example of the breed - both inside and out - and breed in a way that prevents the gene pool from changing over time. For this, all the genes in the dogs of the present generation must be replicated and packaged into the offspring produced for the next generation. The particular genes each individual inherits will be different, but the frequencies of the genes in the gene pool should stay the same over time. For all those things that are a consequence of many genes, some of which might interact, getting this transfer of the gene pool into the next generation is critical. If the next generation includes only part of the gene pool, then you won't get the same traits. Remember, for same traits, you need the same genes. If the genes change, the traits will change. 

Breeders of commercial domestic animals know this. They develop breeding strategies to prevent their gene pool from changing over time. This is the purpose of rotational breeding. If you want to breed sustainably, you must take steps to prevent the gene pool from changing over time.

The dog fancy does not do this. We select for the traits we can assess, with no worry about protecting the genes for the traits we can't. In short, we do not breed in a way that will prevent the gene pool from changing over time. In fact, we apply strong selection for those evident traits by breeding the individuals we deem the "best", and remove the other animals from the gene pool. Consequently, the composition of the gene pool is different in every generation, even if the dogs look physically the same. That is what we are referring to when we talk about loss of genetic diversity. Furthermore, not only the composition of the gene pool changes, but the expression of those genes changes because breeding to related animals produces inbreeding, which is an increase in homozygosity. There are always mutations hanging out harmlessly in the genome of every animal, so producing homozygosity is going to result in changes in characteristics. And indeed, this is the endless battle of the breeder, who is breeding only the "best" animals, yet producing animals that are flawed in some way. We understand why this happens. 

To keep the dogs the same, both for things we can see and things we can't like health, we need to prevent changes in the genes. 

In the dog fancy, this is the elephant in the room. We. Do. Not. Do. This.

The gene pool of every dog breed is changing every generation because we breed only a small fraction of the animals produced by the previous generation. Because genes cannot be added to the gene pool (this is the closed stud book), the gene pool will lose genes that are not replaced. If we believe in genetics (and we do!), every gene has some job it's there to do, and if we remove that gene, we should expect that something will be broken. Sometimes it's something obvious, but mostly these broken things create tiny little problems that escape immediate attention but accumulate over time until we have a real issue. This is not rocket science. A grade school child should be able to understand that if you remove all the red M&Ms from the bowl, you will not be able to eat any red M&Ms.

Okay, so dog breeders have not been protecting the gene pools of their breeds, and we have the problems to show for it. (A point of history: this is a legacy of a culture at the time of breed formation that prioritized "purity" over preservation of gene pools, although to be fair this was long before we understood the genetic basis of inheritance.) If the loss of genes every generation results in changes in function or health, what sense does it make to do more of what caused the problem in the first place? We remove dogs from breeding that don't have the traits or function that we want. We think we're "getting rid of a problem." But the problem is the loss of the diversity of genes that are critical to the function of complex physiology, behavior, and biochemistry. We created our problems by not protecting the gene pool of a breed, and we are trying to return the breed to health by changing the gene pool even more, and in ways that we have no way to know. 

​Ask our grade school child how we fix this. If the red M&Ms somehow made all the other M&Ms taste better in some invisible way, and the remaining M&Ms just aren't as good without the red ones in the mix, the only way we will get that great taste back is by replacing the red M&Ms that were lost. Now, they will come from a different bag than the original ones. But they're exactly the same. Put those in the bowl and we can recover what we started with. If we for some reason insist that we cannot add any M&Ms from a different bag, then we are permanently stuck with our red M&M deficit and a bowl of inferior-tasting M&Ms.

The health problems in purebred dogs are a consequence of inadequate genetic management that resulted from adopting breeding strategies that do not protect the gene pool. Our inability to solve these problem despite decades of diligent effort is a predictable consequence of breeding strategies that do not restore the gene pool to its original condition. Notice that DNA testing is not going make dogs healthier, because we are still not doing anything to protect the gene pool from deleterious change, much less restoring it to that of a population of healthy dogs.

We must understand genetics to breed dogs. But we must also understand evolution. We do pretty good with the genetics stuff. But are failing miserably at the evolution part, which is the implementation of genetic management. The tool for this is population genetics, something most breeders know nothing about, or understand "just enough to be dangerous," as the saying goes. If we had relatively healthy populations of dogs, a general understanding of population genetics would be fine. But what we have are breeds that have been under strong genetic selection but without genetic management, so gene pools have changed every generation without guidance and with ineffective protection of diversity. These gene pools are well and truly broken.

We will not make dogs healthier by "health testing," and you should now understand why. We are also not doing "preservation breeding," and that you should also understand. Research will not solve the health problems of dogs, because the problem is not the disease, it's the loss of the genes necessary for all the complicated stuff that needs to happen in a dog over an entire lifetime - birth, growth, immune defense, behavior, and an infinity of other events and processes that are the essence of life. If 20% of the genome has been lost from those original dogs that had both good type and good health, we will not have those original traits, and we don't. We have carefully bred to protect the genes for type; we have deliberately bred in a way guaranteed to lose genes for everything else. 

The problems have been evident for a long time. Biologists have been explaining why things are not working well. But there's no mystery here. Even our grade schooler can understand this problem and how to fix it. If breeders understand genetics and evolution, they should certainly be able to do this too.

I keep seeing the statement in the title, usually in the context of a discussion about the need to improve genetic diversity of a breed with a cross-breeding program.

The people that say this reveal their poor understanding some basic principles of genetics that should be elementary level stuff for every dog breeder. But apparently not. This statement is false, and here's why.

Most of the hundreds of genetic disorders identified in dogs are caused by single, recessive mutations. A dog with one copy of the normal allele and one copy of the mutation will usually be unaffected and healthy. A dog that inherits two copies of the mutation will not, of course, have a copy of the normal allele, so whatever that gene is supposed to do in the body isn't going to happen. It will either be apparent as a disorder of some sort, or it will not be evident at all if the effects are subtle or do something like reduce fertility, or slow down some enzymatic reaction, or slow growth rate. But apparent or not, it can be expected that if a dog gets two copies of a mutation, there will be some sort of functional deficit.​
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The fact that different breeds rarely share the same mutations is also the reason why mixed breed dogs are, on average, healthier than purebred dogs. While they might carry more mutations, those mutations are much less likely to be homozygous and therefore be expressed as disease (Donner et al 2018).

​The offspring of a cross breeding will produce offspring that will carry some of those mutations. If those dogs do lots of breeding, they will produce many copies of those mutations packaged in puppies that will enter the breeding population. The way to keep those mutations from being a problem, is to not make hundreds of copies and distribute them throughout the population. Keep them few and rare by nixing those popular sires.

REFERENCES

Donner J and others. 2018. Frequency and distribution of 152 disease variants in over 100,000 mixed breed and purebred dogs. PLoS Genetics  14(4): e1007361.  DOI: 10.1371/journal.pgen.1007361

​I asked the members of my ICB Breeding for the Future Facebook group to rate their understanding of genetic management and that of the people in their breed.

Like the folks that live in the mythical town of Lake Wobegon, where everyone is “above average”, most people responded to the "Rate Yourself" post with a score of 3 or more on a scale of 1 to 5. And pretty much everybody said that the overall level of understanding of the people in their breed was low (lots of 1s for this).
 
The latter response is very worrisome. Here’s why.
 
 Find your breed on this graph, which is the genomic (from DNA) inbreeding of a large number of purebred dog breeds. These data are consistent with data from several other studies of different populations, so we can assume that this is a fair representation of inbreeding in these breeds.
 
The green line is inbreeding of 6.25% (mating of first cousins), yellow is 12.5% (mating of half sibs), and red is 25% (full-sib mating). (I made this graph to highlight the data for Cavaliers for another post; the black line at about 41% is the average inbreeding of this breed.)
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​This means that, because of the facts of basic genetics, you cannot “preserve” a breed in a closed gene pool. You might breed in a way that attempts to limit the damage to the gene pool, but you cannot preserve a breed if alleles necessary for function and health are lost from the gene pool every generation. You can be a “responsible” breeder," and make choices that attempt to limit the damage, but you cannot be a ”preservation” breeder, not when more genes necessary for the body to function are being lost every generation. 

Can we at least say that we are breeding responsibly, i.e., making breeding decisions that will limit the damage to a breed’s gene pool? Let’s look at some data.

These graphs are from Lewis et al (2015) and are based on the pedigree records of the UK Kennel Club. Note that the data were not digitized before 1980, so the graphs start there, and the COIs are much lower than actual values because the ancestors from 1980 back to founders are not included in the calculation. Also, ban on importing dogs into the UK was lifted in 2000, and the incomplete pedigree data for those dogs make it look like the average population inbreeding is going down after that, which is probably not the case.

The blue line is the average COI computed from the pedigree data. The red line is the level of inbreeding that would be expected if the dogs in the population were breeding randomly. If breeders were making a strong effort to avoid inbreeding, the blue line would be below the red line; if breeders are preferentially breeding dogs that are more closely related than average, the blue line would be above the red line. 

These graphs tell us about the overall breeding strategies being used in each breed. Breeders are preferentially inbreeding. (I have grabbed a few of the breeds that have a population large enough to show a trend instead of a line that goes all over the place.)

We want to preserve breeds. We want to produce healthy, long-lived dogs. But look at the data. How are we going to do this?

In response to the ban on breeding Cavaliers and Bulldogs in Norway, the clubs have responded that the breeders are in the best position to solve the problems and are working hard to do this. But inbreeding will continue because it is unavoidable in a closed gene pool. DNA testing can prevent disorders caused by a single, recessive mutation for which we have a test, but we do nothing to control the many other recessive mutations we know are lurking in the gene pool, and selection is doing a poor job of managing the problems that are likely polygenic. Plus, we are preferentially inbreeding, increasing the risk of producing genetic disorders from mutations we don't yet know about.

I noted up at the top that, in a survey of the people in my Facebook group, ICB Breeding for the Future, most people rated their understanding of the principles of genetic management and breeding for health at a 3 or higher on a scale of 1-5, where 5 is highest. They also overwhelmingly rated the average understanding of the people in their breed at 1. 

If we want to have purebred dogs, we need to solve some serious problems, we need to get it right the first time, and we need to do it soon. The kennel clubs say “We can do this,” but breeders assess the general level of genetic management expertise of their colleagues as rock bottom. 
 
I can probably count on one hand the number of dog breeders I know that have enough expertise in population genetics to “know what they don’t know,” and all of those people are professional scientists that happen to also breed dogs. Beyond that, there is an army of “Facebook experts” - people that might know something about little bits of a topic but dispense advice as if expert. Invariably, they say things that are incorrect, because they don’t know enough to appreciate the nuances, complications, and depth of concepts. They don’t know what they don’t know, and most people don't know the difference. These experts don’t do any topical coursework (e.g., I don't see them in ICBs online courses for breeders), and they usually have no background in science at all. What they “know” has mostly come from things they read on Facebook written by other people with no expertise. 

If you are tackling a very difficult problem, and if getting it wrong could result in catastrophe, these Facebook experts are extremely dangerous. Most breeders in my survey judged the expertise in their own breed as very poor. Most probably wouldn’t know good advice from bad; they are likely to be most swayed by things that sound “logical” or “make sense”. But their perspective is on managing the genetics of individual dogs. The genetics of populations are quite different, and indeed “the right thing to do” can often be counter-intuitive. You’ve heard that you should only “breed the best to the best”, but this will actually make it harder to improve traits and will ultimately lead to extinction of the population. In fact, this is why we are in this difficult spot, and continuing to use this breeding strategy is the hammer that will sink the last of the nails into the coffin. This is not an opinion; this is a necessary consequence of the mathematics behind population genetics. If you don't know this, then the "best to the best" advice seems like a good thing to do. But it's not.

The Norwegian kennel and breed clubs argue that they can fix the health problem of Cavaliers and Bulldogs by continuing to do the things they think will work. They haven’t worked so far, and they won’t. But apparently they don’t know that.

The Norwegian court offered that crossbreeding to solve the health issues would be allowed, but the feedback on Facebook has been adamantly opposed to even considering cross breeding programs. So, if the Norwegians have a plan to fix this without crossbreeding, I would like to hear how they will do it. 

The breeds in the spotlight in Norway have to come up with a plan to address the issues that put them in violation of the Norwegian Animal Welfare Act. The Norwegians are on the hot seat right now, but every breed has an inbreeding problem that is incompatible with sustainable breeding, incompatible with “preservation” breeding, and incompatible with health. What breeds have a plan to address their growing list of genetic health issues, which will only continue to grow? How will they know if their plan will work? What will they do if it doesn’t?

Purebred dog lovers face two huge challenges. First, we must fix the significant inbreeding problem that imperils  essentially every breed.

Then, once we have inbreeding down to a reasonable level, we need to breed sustainably, which means we have to  control inbreeding and loss of genetic diversity. To do this, breeders will need to understand population genetics, which provides the tools used for the genetic management of animal populations.

Are you thinking you already know a lot about population genetics? Among the essential topics you should be able to explain and discuss are these, for example: linkage disequilibrium, founder genome equivalents, effective population size, the Hardy-Weinberg equation, heritability, fitness, mean average kinship, observed and expected heterozygosity, and genetic drift.

One basic measure of the health of a breed is the size of the population. Large populations are likely to have more genetic variation than small ones (but not always!), and the large number of individuals buffers the population to rapid genetic changes.. This graph shows data for registrations by the UK Kennel Club from founding (1945) to the present. My data for AKC registrations are limited, but I have included them here for information.

The data for the UK Cavaliers reveal details about the history of the breed in that country. The population size increased after it was recognized by the Kennel Club, slowly at first, then very rapidly from about 1970 to 1989, when yearly registrations reached 15,833. From 1990, registrations have generally decreased through about 2010, and since then the decline has been steady and steep. In 2020, 2,967 dogs were registered, a level not seen in the breed since about 1970, a half century ago.

One concern about a declining population is loss of genetic diversity. This can be mitigated if breeders are careful to avoid inbreeding and they balance breeding across the population.  

The graph below displays the observed level of inbreeding in the UK breed population between 1980 and 2015 (in blue). The red, fuzzy line is the expected level of inbreeding in this population if the animals were breeding randomly over the same period of time. The pedigree database for this analysis (which is from Lewis et al 2015) only extends back to 1980, when digital records began. While this graph is useful to detect patterns in inbreeding levels in the breed population over time, the levels of inbreeding on the graph are much lower than what we know to be more accurate inbreeding from DNA analysis, which, as noted above, currently average about 41%

On this graph, if the observed level of inbreeding is higher than the inbreeding expected from random breeding, this indicates that breeders are preferentially inbreeding; i.e., choosing to pair dogs that are more closely related to each other than the average level of relatedness in the population. This also reveals that breeders could be producing puppies with lower levels of inbreeding by pairing individuals that are less closely related.

Note on the graph that the mean inbreeding coefficient decreases after 2000. This is the result of dogs imported after the restrictions to imports were lifted in the UK in 2000. These dogs have only three generations of ancestry in the UK pedigree database, so offspring they produce will appear to be much less inbred than they really are. Remember - in a closed population, the average level of inbreeding can ONLY increase over time. 

(These data are from Lewis et al 2015, and are slightly different from the registration records I have.) 
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Inbreeding results from mating related dogs. Nothing can damage the genetic health of a population faster and more dramatically than a popular sire. This is a dog that produces a disproportionate number of offspring, populating the breed with a large number of offspring that all share half of his genes; i.e., they are all half-siblings. But, just like every other dog, the popular sire carries unknown mutations, and these will invariably result in a genetic defect a few generations down the road. Not all of these defects will be apparent to breeders; mutations that reduce fertility, shorten lifespan, or affect behavior are just a few examples of the ways these unidentified mutations can burden the health of the breed. 

​As in most breeds, the CKCS has popular sires that produce more than their fair share of offspring. These tables show that the most prolific sire in 2020 produced 30% more litters than the next most prolific sire, and 100% more than the dogs ranked 3 through 5. In terms of lifetime contribution, the top sire in 2020 produced twice as many litters as the second  ranked dog (111 vs 60). To understand the true consequences of popular sires on the genetics of a population see my article The Pox of Popular Sires. 

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This chart also reveals the impact of the most popular sires in the breed. For instance, the top 5% of sires produce on average about 20% of the puppies in each year. Likewise, the top 50% of sires produce about 80% of the puppies, so the lower 50% of sires account for only 20% of the puppies.
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Relating to the unbalanced use of sires is the tendency to restrict breeding of sires more than dams. This is revealed in this graph of the number of sires and dams producing the puppies of a particular year. In recent years, the number of females producing litters in a year has declined dramatically, which probably reflects at least in part the decline in the size of the population. The number of males producing litters has been relatively stable for most of the last 30 years, but in the last decade has been falling.
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With the exception of the first graph, which includes data for AKC registrations for a few years, the data analyzed here are from the registry of the UK Kennel Club. However, this breed is popular in many countries in the world, and we cannot assess the true genetic status of the breed without including those data (or as much as possible) as well. If you have access to data for other countries, please contact me so I can incorporate them in these analyses. 

This is the first of what will be multiple installments that will shed some light on the genetic status of the Cavalier King Charles Spaniel. This information is essential to understand the history of the breed, and is even more critical or sound genetic management into the future. There are a few things already evident here that breeders should consider, perhaps most importantly, the declining registrations in the UK. As the country of origin, a healthy representation of the breed in the country has cultural importance. 

Related to questions about my previous Cavalier post, I still do not have the data necessary to determine the original size of the gene pool of the breed. I am chasing down ancestors and trying to connect ancestors, and I will let you know when have an estimate. 

Stay tuned - part 2 is coming soon!

There is growing recognition that loss of genetic diversity from the gene pool of a breed over the generations is having the unwelcome result of increasing the burden of health issues. The geneticists claim that the remedy for this is crossbreeding that will introduce new diversity into the breed. However, there is much fear among breeders that cross-breeding might improve genetic diversity, but it will destroy breed type. 

Let's have a look the results of a breeding program that did a cross that most would think is crazy, of a Boxer to a Pembroke Corgi. 

​Cattanach bred a white Boxer named Polly to a Pembroke Corgi with a natural bobbed tail. They produced a litter of seven puppies that all looked alike, with a fawn color and piebald white markings, and traces of a black mask on some. Five had bobbed tails of various lengths and two had normal tails. In structural traits, the Corgi influence predominated. The legs were short and coats longish, reflecting the influence of those dominant genes. The head resembled that of the Corgi, but with drop ears ( at 7 months the ears of one pup were erect) and eyes more like those of a Boxer. These pups were dubbed the "Borgies" and apparently were unbearably cute. 

​Two of the female hybrid pups, Dolly and Tess, were chosen to be backcrossed to one of Cattanach's male Boxers. They produced 9 and 7 puppies respectively. These varied from Boxer-like to "Borgi", with legs of varying length and about half with bobbed tails (7 of 16). 
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For the second backcross, a solid white female was chosen from the first backcross puppies as carrying the best suite of Boxer traits. The sire had to have good type but also no risk of producing white puppies that could potentially be deaf, so it could not carry the gene that produces the white "flash" markings on most show dogs. With this dog, Cattanach then predicted what to expect in the progeny that would be produced from a cross to Jane, the typiest of the first generation backcross puppies:

The second backcross produced eight puppies, seven of which survived, and all with flashy white markings. Five had bob tails and the tails of the rest were normal. Cattanach said of these that "In general appearance they all looked like Boxers."

These are the seven pups from the second backcross litter at 10 months. Four of these inherited bob tails; the rest were docked.

For the fourth generation, the best male from the second backcross litter was bred to a bitch that produced a puppy that, apart from a long tail, Cattanach judged to look like a pure Boxer.
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​At the end of the project, Cattanach provided the details of all of the breedings to the UK Kennel Club with a request to consider them for registration. The KC agreed to register the fourth generation as Boxers and the previous ones as crossbreds.

Descendants of Cattanach's bobtail Boxer breeding experiment can be seen in the European show ring today.

How was it possible to cross a Corgi with a Boxer and get puppies with good Boxer type so quickly? Look at the genetics.

The Corgi x Boxer cross produces puppies that are 50% Corgi and 50% Boxer genes (inheriting one chromosome from each parent), the "Borgies". The gene for short legs is dominant, so they are all short. In the first backcross, the puppies will pick up more Boxer alleles, averaging 75% Boxer and 25% Corgi. Depending on which alleles each pup inherits from each parent, the traits in these puppies can vary widely, some looking much like Boxers. Among these was Jane, a white bitch with very good Boxer type that Cattanach used for the next backcross. As expected, if the best of the pups from the first backcross is crossed again to a Boxer, there should be much uniformity among the pups because now they carry on average 87.5% Boxer alleles and only 12.5% from their Corgi ancestor. These dogs looked like Boxers.

This is not the catastrophic genetic mish-mash many breeders fear will be the result of a cross-breeding. With some basic knowledge of a few key genes, Cattanach was able to predict what each cross would produce. This allowed him to get quickly from initial breed cross to producing entire litters of dogs of that are unmistakably Boxers, with no hint of their cross-bred ancestry, and some even of show quality.

Cattanach was interested in transferring only a single gene, and his breeding strategy was centered on that. He was able to make progress quickly in this project because he knew that the traits that made the Corgi look so different from the Boxer would be easy to select away from. A breeder would use a different breeding strategy if the goal was to improve genetic diversity, but the same principles would apply. 

The dog fancy is facing unprecedented challenges to improve the health of purebred dogs. These problems can be traced to the imposition of a closed gene pool on the population and selection for traits that compromise health. Because inbreeding is so high in all but a few breeds, improving health using selection within the existing  gene pool is simply not possible. You can't solve a health problem by selection if the alleles you need are no longer in the gene pool. The only option at that point is to restore the genetic diversity of the gene pool of each breed by crossing with dogs that carry the needed variation. There really is no other way to do this. And as this experiment shows, the result will not be a breed-destroying catastrophe if done with proper planning. Take the time to understand the genetics and seek the guidance of experts that can map out a breeding strategy that will get you from cross to show quality dogs in the shortest number of generations.

If your breed has high inbreeding (okay, Sloughi, you're good; this is for the rest of you), crossbreeding can restore the genetic diversity that has been lost over the generations. Let go of fear and believe in genetics. 

What about registering the puppies? Cattanach was able to register his by request. These days, the kennel clubs are under the gun to improve health "or else" (see the court case in Norway). Because there is no other way to do this than crossbreeding in most breeds, I expect there will be little resistance to registering puppies that descend from crossbreeding programs in the future.

There are a few other examples of crossbreeding programs in dogs that I will be summarizing as well. I will post links here when those are available.

The Mayo Clinic is a non-profit medical institution in the United States that is famous for its integrated approach to solving difficult medical problems. Patients at the Mayo Clinic have usually run a gauntlet of medical specialists without success at cure, treatment, or even diagnosis. For these individuals, the Mayo Clinic is a last hope.

The Mayo Clinic is well known because it has been exceptionally good at solving the problems of the most difficult patients. It does this using an integrative approach to health care that might involve specialists in many fields that work together as a team to achieve diagnosis and treatment when specialists working independently have failed. Their extraordinary success using this integrated approach draws patients from around the world.

I think we need something comparable to the Mayo Clinic to help us address the growing burden of health issues in purebred dogs. Here's why.

Breeding bans for violations of animal welfare laws are not designed to address the underlying problem, which is the high burden of diseases in purebred dogs. They simply prevent the production of animals that are likely to suffer. Managing and eliminating the health issues is left to breeders and purebred dog organizations such as kennel clubs. However, breeders lack the expertise, and often the will, to address these problems effectively. For example, breeders have been enthusiastic adopters of DNA testing to identify known mutations in their breeding stock, but the common assertion that a dog is healthy if it is "clear" of mutations is untrue. Furthermore, using this information properly can be tricky (e.g., mutation vs linkage tests), and advice from fellow breeders on Facebook can run the gamut from factual and informative to just plain wrong. In any case, because dogs surely have many more mutations than we know about and can test for, DNA testing will not make dogs healthier because they are so specific. For instance, a breeder that dutifully runs the available mutation tests, then breeds to a popular sire, is simply exchanging a known risk with an unknown one.

Faced with a health issue, the temptation of breeders is usually to assume that it is caused by a gene, with the result that they identify individual issues and search for solutions, one problem at a time. If a genetic disorder pops up in a breed, the scenario would be to search for the mutation, develop a mutation test that can be used on individual dogs, then avoid breeding dogs together that share the same mutations. This strategy can be effective if the disorder is caused by a single recessive mutation, but many problems are not; for these, affected animals and maybe also their relatives are removed from the breeding population on the assumption that there is some underlying genetic cause that should not be perpetuated. Breeders have been trying to manage many disorders this way, such as epilepsy, cancer, and renal dysplasia, but with little success. The consequence is that dogs (and their genes) are removed from the breeding stock, which reduces the size of the breeding population and increases the rate of inbreeding, both of which act to increase the expression of genetic disorders. Thus, breeds are stuck in a loop in which the actions of breeders to reduce the risk of genetic disorders actually increases the likelihood that some other issue will appear. It's an endless game of genetic whack-a-mole that is slowly driving breeds closer and closer to point where genetic deterioration will be severe enough that the breed goes extinct.

There are breeds that appear to already be at this extinction point. A very high percentage of Dobermans die of fatal DCM (degenerative cardiomyopathy), and recently the trend has been towards deaths in younger and younger dogs.  Flatcoated Retrievers and Bernese Mountain Dogs rarely live past middle age, because they are stricken down by cancer. Most Cavalier King Charles Spaniels will suffer from mitral valve disease, and an early onset form of the disease takes dogs in their prime (Lewis et al 2011). Upwards of 70% of Cavaliers are also the victims of painful neurological conditions, Syringomyelia and Chiari Formation, which are also becoming increasingly common in other breeds with shortened muzzles and a tendency towards domed skulls (e.g., French Bulldogs, Brussels Griffons, Chihuahua). For these breeds and many others, the health issues common in the breed challenge the ethics of continuing to breed them.

We will not begin to stem the tide of health issues in purebred dogs by doing more of what we already do. In response to the ruling by the Norwegian court that banned the breeding of Cavaliers and Bulldogs, the Norwegian Kennel Club said that it would continue to work with breeders to improve breed health through health requirements for breeding and other undefined measures. Similar statements supporting the Norwegian Kennel Club's position were forthcoming from the FCI, Australia, and other kennel clubs around the world. Breeders and kennel clubs are going to double down.

What is missing in these statements is the recognition that the underlying problem is not with the genetics of individual dogs, but rather it is a problem of genetics across the breed. For many decades, most purebred dog breeds have been part of a registration system that is strictly closed to the introduction of dogs from unregistered parents. The result is a genetically closed population, a group of animals trapped on a genetically isolated island. All individuals are necessarily related, having descended from the same original genetic founders, so all breeding will be to a relative. Each breed is a genetically closed population from which genes can be lost through selective breeding or just by chance, but the genes lost cannot be replaced because of the closed registry. The result is that the gene pool shrinks relentlessly, and the population becomes more and more inbred. Eventually, genetically closed populations, like those of purebred dogs, suffer an increasing burden of health problems, low fertility, and shortened lifespan until, eventually, they simply go extinct. This is the road most breeds are on, and the kennel clubs have said nothing in their recent statements about the breeding ban in Norway that suggests a plan to change this trajectory. In fact, doing more of the same, even harder and more carefully, will actually make things worse.

We have a complex problem to solve, one which the stakeholders - breeders and clubs - are simply not equipped to address. Each breed has its own unique set of issues, and our current strategy is to focus on one or a few of these at a time. However, it's not the individual problems that need to be addressed, but the underlying cause, which is common to all breeds. Purebred dogs are trapped in closed gene pools that force inbreeding. We will not solve the health problems in dogs until we abandon the closed stud book that prevents replacement of genes that are systematically lost every generation. 

Opening the stud books would slow the pace of new problems, but restoring health to the many breeds that are badly damaged will require a systematic and well-planned strategy. Unfortunately, however, there is nowhere for breeders to go for help.


Here is where I think we need something for dog breeds that is comparable to the Mayo Clinic. Note that I specified "dog breeds" and not individual dogs. The health problems of dogs are a consequence of the genetic health and structure of the population of animals in the breed, and the solution must first be directed at the breed population, not the individual dogs. The approach must be integrated and specific for the circumstances of each breed. Coming up with the right plan will require a broad range of expertise.

The genetic rescue of the Norwegian Lundehund has taken this approach. Inbreeding of the Lundehund is 80%, the highest ever recorded in a dog (perhaps also in any mammal?!!), and the breed suffers from extremely low fertility and a gastrointestinal disorder than can be fatal. Before designing a breeding plan for genetic rescue, a team of scientists performed genetic analyses on the pedigree database and another team analyzed genotypes of both the Lundehund and breeds identified as potential candidates for cross breeding. Using demographic information, genetic modeling showed how different breeding strategies would affect the efficiency of a breeding program, e.g., how many animals would be required and how long would it take for gains in genetic diversity. Each animal used and produced is evaluated for health and relevant traits, and additional breedings are planned based on the parameters of the genetic model being followed. Done properly, with good scientific oversight, a genetic rescue program like this can demonstrate the effectiveness of the breeding strategy in two generations. For the Lundehund, the second generation backcross has produced healthy animals of good  type that also carry new genetic diversity that can be integrated into the breed population. 

To tackle the health issues of purebred dogs, we need to take an integrative approach. The diseases in individual dogs reflect choices made by breeders, constraints on breeding options imposed by the closed gene pool, division of gene pools based on geography, different preferences for type, the varied purposes for which the dogs are bred (show, working, pet), how breeders are choosing to manage genetic health issues, and many other things. The issues will vary by breed, as will the potential solutions. Tackling these problems will require the expertise of teams of scientists that can work out the critical problems and the range of practical options for addressing them. There will need to be tracking of animals and followup, periodic evaluation of progress, tending of pedigree databases and genotype data, and (perhaps most important of all) education of breeders so they can be full participants in the solutions for their breeds and have the knowledge to carry the breed forward with oversight when genetic restoration is successful.

A place like this does not exist, yet it is desperately needed now, to help breeders tackle health problems before more breeding bans are imposed on potentially dozens of breeds. Cornell University, my alma mater (PhD.), recently received a $30 million gift to launch the Cornell Margaret and Richard Riney Canine Health Center at the university's excellent veterinary school. Another gift of $12 million will establish the Duffield Institute of Animal Behavior at Cornell. These funds fortify what already was a strong concentration of resources in canine health and genetics at Cornell. But neither will address what is arguably the most pressing issue affecting the health of dogs: the burden of genetic disorders that result from traditional but outdated breeding practices and ineffective strategies for preventing disease. ​While disease research has improved our understanding of the illnesses suffered by dogs, it rarely has substantial impact on health because it doesn't alter the landscape of underlying issues that result in the production of genetic disease in the first place. To make a difference, we need an approach that focuses not just on the dogs, but also on the breeders. Breeders need access to education, to up-to-date data about the genetic status of their breed, and (especially) to expert guidance to replace the blizzard of opinions available on Facebook as a source of factual, relevant information.

Many breeds are now or will soon be at a crossroads - they must solve the serious health problems in the breed or face a ban on breeding. Addressing these problems will require creation of something similar to what I have described here, and it will require a significant initial investment, one that breeders will likely be unable to meet. Philanthropy can recognize the health problems of dogs because they are visible; it it harder to see the connection of the health problems to the underlying issues of inbreeding, closed gene pools, traditional but outdated breeding strategies, and misunderstandings about the proper use of DNA testing.

I don't see the problems facing dogs and their breeders being solved without a Mayo Clinic-like institution where a concentration of expertise can tease apart the layers of issues that must be addressed in order to restore dog breeds to health.

We know that genetic rescue is possible, but the infrastructure necessary to do it for more than a breed or two at a time simply doesn't exist. We know what we need to build if we can find the resources. The challenge now is to identify those that have a commitment to improving the health of dogs and can help pull together the resources to move this forward. 

We do DNA testing to identify carriers of mutations so we can avoid the 25% risk of producing a puppy that is homozygous for the mutation. We know that every animal has many mutations lurking in its genome, and we can't test for the ones we don't know about. But the probability of producing a puppy homozygous for an unknown mutation is going to be the same as from a known one.

Cavaliers are all so closely related to each other that the average inbreeding produced in a puppy is 40% so the risk of homozogysity in a mutation is 40% as well.

Now, think about this.

You do your DNA testing to avoid producing a puppy affected by a known mutation, which you can prevent entirely by not mating two carriers.

But for all those unknown mutations in the genome, the risk of producing an affected puppy is the same as the average inbreeding, which  is actually 40%, not 25%. ​

DNA testing allows us to test for carriers of mutations so that we can avoid this 25% risk of producing affected animals. But when all the dogs in the population are closely related, the average inbreeding of a litter is 40%, far above the 25% risk you're trying to avoid. You can see from this that health testing in Cavaliers is really not accomplishing anything except costing you money.


The problem with science is that it's true even when it's not what you would like to believe. The data for Cavaliers are clear. No amount of selective breeding is going to improve the health of this breed. You might temporarily reduce the incidence of some specific nasty mutation temporarily in a part of the population, but everybody is in the same genetic pot. Inbreeding will continue to go up over time, the small genetic differences between populations will disappear over time as genetic diversity declines, and eventually you will no longer be able to produce healthy animals. In fact, this is where Cavaliers appear to be now.

Cavaliers are in deep trouble. There are plenty of other breeds in similar shape, but what matters to those that love Cavaliers is whether it can be saved. We know that we can only restore health by restoring genetic diversity. We do know how to do with without losing breed type. Animal breeders have been doing this for hundreds of years to produce quality animals that can be nearly identical, with inbreeding levels in the single digits. It can just as easily be done for dogs as well, and Cavaliers are a perfect candidate. But not in a closed gene pool.

I have to say that what I have read on social media this week makes me worry that breeders will continue to argue about the arrangement of the deck chairs while the ship slowly slips under the waves. I hope I'm wrong. 

REFERENCES

Dreger, DL et al, 2016. Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping. Disease Models & Mechanisms 9(12): 1445-1460. https://doi.org/10.1242/dmm.027037

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

In response to your queries regarding restoring dog breeds to health so as to meet the guidelines of the Animal Welfare Act, we make these recommendations.

ACTIONS

1) Open the stud book

2) Do not breed closely related dogs (a kinship cutoff of 0.10 will protect type and minimize risk)

We are happy to provide additional guidance at your request.

Norway's ban this week on breeding of Bulldogs and Cavalier King Charles Spaniels (see my previous post about this) has rocked the dog world, not just the dog fancy, but also the larger global community of dog lovers. Certainly among breeders, there is anger and despair, and loud calls to organize and "fight back" against what is seen as an attack on breeders of purebred dogs.

It's not helping that there is far more misinformation out there than facts. Rumors, assumptions, and opinions repeated a time or two on social media get shared more widely as they become more outrageous. People are posting all sorts of (mis)information that they got from ***somewhere***, to that point that a trickle of misinformation has grown to a torrent. The result is fear and confusion, and a growing sense that an entire community is passing through the stages of grief.

The best solution for this, of course, is facts. I am wading through the swamp myself, and I STILL have yet to find a copy of the court ruling in ENGLISH so we can actually know what it says. (Norwegian peeps, can somebody come up with this?) While we still lack clarity on many issues, I will share here a few things that should cut down a bit on the misinformation flying around. The facts should also confirm that purebred dogs are not doomed to extinction and there IS a way forward for for breeders.

First, the court ruling is based on Norway's Animal Welfare Act, which provides for the protection of the health and well-being of animals. Most countries have similar legislation. 

In this case, the court cited violation of provision 25 of the Animal Welfare Act. You can see the entire document here on the governmental website for this legislation, but here are a few key excerpts.
​

​A few salient points about this.

First, this is not a new law.

Also, it is not directed at dog breeders. In fact, it stipulates up front that it protects the welfare of everything with a backbone (e.g., mammals, birds, fishes, etc) as well as some invertebrate groups including octopi and honey bees. Yes, it protects both dogs and honey bees.

It explains that the legislation reflects our responsibility to respect the value of animals and to ensure their humane treatment, and it provides some basic guidelines for doing that.

The section relevant to the breeding of dogs is 25.

That's the entirety of section 25 of the Animal Welfare Act cited by the court. It's only a few sentences, and it makes just a few stipulations. Most basically, it states that
​

This seems like a perfectly reasonable requirement that most people could support. To avoid running afowl of the Norwegian law, the dogs we breed must be "robust, "function well", and "have good health".

Again, I haven't seen the court case so I don't know what specific information was presented about the health of these two breeds. But there is no shortage of data documenting the serious health problems in these breeds. Bulldogs are brachycephalic, with a shortened muzzle prevents temperature regulation and a throat anatomy that restricts breathing to the point that it can result in suffocation. The snoring that many breed lovers find endearing is the sound of the air fluttering as it moves over structures in the airways that block air flow. A snoring dog is having trouble breathing. Bulldogs are also at the top of the list of breeds that suffer from hip dysplasia, with 73.5% diagnosed as dysplastic in the OFA database, and essentially none are excellent. There are also issues with skin fold disease, spinal problems, and other disorders, but even the short list of the most serious problems would be enough bounce the breed off the list of breeds that could be considered "robust" and with "good health". 

For Cavaliers, the problems are equally serious and well-documented. Mitral valve disease is terminal and afflicts almost all Cavaliers by the age of 10 years. The breed is notorious for the neurological disorders Chiari-like malformation and syringomyelia, which can result in a lifetime of severe pain and even paralysis.

Of course, not all dogs in either breed will suffer from a particular disorder. Disease prevalence is statistical. There will almost always be a few individuals out on the tail of the bell curve that are not affected. The few individuals that escape disease might live long, healthy lives, but these are not evidence of breed health because, of course, most of the afflicted animals in the body of the curve have died and are no longer around to be represented in the population.

I would imagine this is the sort of evidence the court considered in deciding whether these two breeds were in breach of the Norwegian Animal Welfare Act.

One last thing. There is lots of ink being spilled on issues that are not relevant. Most of the discussions I am seeing about this court ruling center on one of the issues I outline here (e.g., there is no problem in the breed because "I have a 12 year old Cavalier that has never been sick a day!"; or "This is an attack on purebred dog breeders by the animal rights wackos.", except that it's not.)


Breeders can't have an effective discussion about how they can bring their breeds into compliance with the law unless they focus on the problem at hand. This is not about puppy mills or the extinction of show dogs. The problem is health of the dogs you breed. Focus like a laser on that.

Here's a way to think about this. If there are lots of serious accidents at a particular intersection, the traffic people might decide to put up signs for a 4-way stop. This will drastically cut down on the number of accidents, making the intersection much safer for all. But, the stop signs might result in a line of cars backing up to get through the intersection, making people late for work, or even encouraging people to speed or drive recklessly to make up for lost time. Are these reasons to remove the stop signs? No. You have health and welfare problems to solve.  Ignore all the other potential knock-on issues that are not your responsibility to solve, and leave those to the powers that can do something about them. Your single responsibility is resolving the issues that compromise the health of your breed. Don't waste time and energy arguing among yourselves about how to solve what are clearly complicated problems. Ask scientists and veterinarians for help.

We all want healthy dogs. You can do this.

Science knows how to solve these problems.

There is now a published study documenting a breeding program for Norwegian Lundehunds that is achieving success in solving serious health issues of this breed. They didn't have a lot to work with - a small population of dogs globally with an average inbreeding coefficient of 80% (!!!). But under the direction of an international team of scientists, breeders have restored genetic diversity through a cross-breeding program while preserving the traits that make this breed iconic and unique (Melis et al 2022). 

By Carol Beuchat Phd

When people contact me asking for help with coat color genetics, I tell them It's Complicated and refer them to one of the Facebook groups devoted to the topic.

Now when I get a question, I will refer them to this paper. Horray!

Download your copy here.

From many published studies, we know that the heritability of hip dysplasia is usually 0.2 to 0.3. This means that 20-30% of the variation in hip score in a population of dogs can be accounted for by variation in genes, while 80% of that variation reflects the effects of non-genetic - i.e., environmental - factors. (NOTE: This is NOT the same as saying "hip dysplasia is 20% genetic and 80% environment." If you are fuzzy on the meaning of heritability, check out my blog that explains the essentials, "What is "heritability" and why do you need to know?".)

When you choose breeding dogs based on hip (or elbow) scores, you are assuming that a good score reflects "good" genes. But we know the heritability of hip dysplasia is relatively low. When you compare the scores of multiple dogs, only about 20% of the variation in scores reflects variation in the genetics of the dogs. Or, to put it another way, 80% of the variation among the dogs you are evaluating is a consequence of non-genetic factors, about which you know nothing. When you eliminate a dog for a low hip score, it is likely that the score reflects some environmental factor and NOT genetics. Wow. No wonder generations of selection hasn't moved the needle much towards better hips in dogs.

If the goal is healthy hips, we should be able to make a big difference by paying attention to the potential environmental factors that increase the risk of developing dysplasia, because that's where most of the variation from dog to dog is coming from. But what are those factors? It's hard to know because every litter is reared in a different environment, every puppy has different experiences, and there is really little you can control about a lot of these things.

But again and again, I see puppies in situations that can have a HUGE effect on the risk of developing hip dysplasia. It seems obvious to me, but it must not be to others judging by how common it is. I will try to describe it here in a way that should stick in your mind when you provide experiences for your next litter of puppies.

​Toddler Safety
Look at this photo. It depicts a toddler standing on a small table and also standing on a large table.

If this is your todder, one of these images will spur you into action to whip that kid off the table before he falls off or tries to jump. It's that large table, right? Why? Because the distance that toddler would fall is likely to result in injury. The small table isn't so worrisome. The child could crawl off or step down carefully. Even if the child jumps for falls, the distance to the floor is short and not likely to result in more than tears. But a toddler falling from the large table could do some serious bodily damage.

What About Eggs?
You've probably seen those high school students learning a bit about physics in an egg dropping contest. The goal is to drop an egg from a particular height without it breaking. Close to the ground, it's easy. But as the egg is dropped from greater heights, the accidents start to happen. Everything stays the same except the distance the egg falls, but the farther it falls the greater the force of landing. If the students don't come up with a clever way to protect the eggs from the force of impact, their egg will be a fatality. 

This is just like the toddler on the table. The toddler's skeleton, muscles, and ligaments can accommodate the force of a short fall. But from greater heights, the force of impact will also be greater and at some point will exceed the limitations of the body. Parents see the danger intuitively and make sure their kids play in the part of the playground designed for the little folk where there are no opportunities to fall far enough to do damage.

,​
What About Puppies?
Puppies are toddlers. Not very big, not very strong, not very coordinated, and not even fully developed. In particular, the joints are cartilage instead of bone. They are not designed to tolerate extreme forces of impact or stress, and they will not be fully ossified until the puppy is about 6 months old. For the first few months of the puppy's life, the joints are designed to tolerate "normal" forces a puppy would experience while running and playing.

The most common cause of cartilage damage in children is from trauma. Sports, accidents, and activities that can result in impact are obvious risk factors for children. The same factors also apply to puppies. 

Let's replace the toddler on the table with a puppy at similar scale. The puppy on the small table can get down without doing major damage because the height is low - the puppy could just step down - and even if it jumps,  the potential force of impact will be small. Most people would see the puppy on the large table at risk of serious injury if it falls or jumps and would snatch it into the arms of safety immediately. Good instincts.

How to Break Puppy Hips and Elbows
If you were among those that would rescue the little puppy from the large table in the picture above, good job! I think most people would.

If you wouldn't allow a puppy to play on a high table, would you allow a puppy to play on some other object that provides a similar risk of a traumatic fall?

So often I see photos of baby puppies, four or five weeks old - very much at the toddler stage - with all sorts of colorful, fun-looking jungle-gym type toys to play on. Perhaps the bright colors, or the perception that these are "fun" things that we enjoyed as children, somehow fails to trigger the parental "danger" instinct. Yet the risk is not different. The expectation is that the puppy will slide down and be deposited safely on the ground at the bottom. But puppies more often fall over the side of the slide, get ejected some distance at the bottom, or worse turn around and simply jump off the side with the steps - which they could not step down as a toddler would. 

If you had to create an apparatus designed to break hips and elbows, this could be a winner.

Look at the skeleton of a dog. When the feet hit the ground, the force of impact is transmitted up the legs to the joints. There are two critical leg joints that are not designed to absorb shock - the hip, which is a ball-and-socket joint, and the elbow, which involves the complex articulation of several bones to allow the leg to move forward and aft. Hips and elbows of adult dogs are designed to survive the trauma of reasonable impact at these joints. The hips and elbows of young puppies are not. 

​Safely Falling Puppies
Browse through the photos below. All of these puppies are falling.

​The running puppy launches itself into the air with the force of the back legs, and the shoulder apparatus absorbs the force of the fall when it lands. The maximum height of that fall is a bit more than the length of the legs, which is usually about half the height of the puppy at the withers. The normal structural features of a puppy should be able to tolerate a fall of this height.

A puppy should be able to jump off something that's about the height of the puppy at the withers, because that's about how far the puppy falls when running. But even if it jumps, the force of landing should be within the design limits of the puppy support structures.

Pay Attention to the Environment
If we want to produce dogs with better hips, we can make the biggest difference most quickly by paying attention to the environmental factors that can increase the risk of developing dysplastic hips and elbows. Health and welfare of our dogs should be our highest concerns, and we can considerably reduce orthopedic pain and suffering by eliminating environmental sources of risk whenever we can.

Put the jungle gym equipment in the garage or donate to the local preschool. Let your puppies have a good time and experience lots of new things, but keep the feet on the ground or no higher than the puppy would "fall" from when running. Try to look at the world from the viewpoint of a puppy - maybe 10 inches high and a few pounds, and just learning how to control those legs.

Genetics matter, but the possibilities of improving hips and elbows are much greater if we can mitigate the sources of that 80% of variation in hip scores that is not accounted for by genes. 

Dr Carol Beuchat PhD

This is a basic but good video about hip dysplasia. I like it because it makes a clear point that puppies are not born with dysplastic hips, and that the development of the socket as the puppy grows is not genetically programmed.

You can learn more about the genetics of dogs in ICB's online courses.

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By Carol Beuchat PhD

It's tempting to assume that bad hips are the result of "bad hip genes", and that you can improve hips through selective breeding by breeding away from the troublesome hip genes.

But nobody can find those genes for bad hips. We can identify genes associated with hip phenotype (normal vs dysplasia) in a Labrador, for example, but those genes are not predictive of hip phenotype in German Shepherds. If there are different genes associated with hip dysplasia in each breed, we have a real mess - a genetic disease that is caused by different genes in every breed. This seems very unlikely.

You can learn more about the genetics of dogs in ICB's online courses.

*** Visit our Facebook pages ***

ICB Institute of Canine Biology
...the latest canine news and research

ICB Breeding for the Future
...the science of animal breeding

Joint laxity (looseness) is a primary risk factor for the development of hip dysplasia. Laxity is the result of stress on a ligament inside the joint, the teres ligament, that attaches the head of the femur to the wall of the hip socket.

If the teres ligament is damaged, the round head of the femur is not held snugly in the cup of the hip joint. Because normal development of the hip is a response to the biomechanical forces on the socket during growth of the puppy, abnormal position of the ball in the socket can result in damage to the rim of the hip socket and the development of hip dysplasia. Proper development of the hip joint depends critically on the head of the femur being properly seated in the center of the hip socket. (You can read more about this in "The 10 most important things to know about canine hip dysplasia.")
​

​How is the teres ligament damaged? Some information about the cause of hip dysplasia in humans can illustrate.

​The hip sockets of dogs and humans are very similar. The head of the femur is firmly held in the hip socket by muscles and tendons. These are so tight, and the teres ligament so short, that at birth, the legs are held apart and slightly bent. If the legs are pulled together, the head of the femur is pulled away from the hip socket as in the illustration below. This puts abnormal stress on the teres ligament and can cause damage that results in laxity in the hip joint. 

The movement of the legs that puts stress on the teres ligament is called extension and adduction - straightening the legs and pulling them together. This is the reason why hip dysplasia is more common in cultures where babies are tightly swaddled than in those that carry infants on the back with the legs around the mother's waist. With this knowledge, new mothers are advised not to wrap up newborns like little burritos but instead swaddle them loosely with room for spread legs and bent knees. 
​

How does this matter to dogs?

The hips of newborn puppies are similar to those of humans.  The hip joint at birth is mostly cartilage, and it will be converted to bone over the first 5 months of growth. At birth, the teres ligament is very short and strong, and it becomes longer as the puppy grows, allowing more freedom of movement in the joint. Also like humans, a newborn puppy on its back will generally hold the legs apart and bent.

However, when a newborn puppy is placed on a surface with inadequate traction, its feet slide right out from under it just as yours do if you walk on ice in street shoes. In the case of the puppy, it tries to walk by pushing backwards with the hind legs, and if traction is not adequate, the legs and even the feet will extend to the maximum. You will notice this happening if you watch puppies in the whelping box and see the pads of the rear feet facing the sky instead of the floor. A puppy (and you) moves forward by pushing backwards. If there is inadequate traction, the legs will extend and adduct, exactly the position that results in damage to the teres ligament in human babies.

Most people that I ask tell me that their puppies are whelped on some material that has good traction. Vet bed, rubber mats, carpet, whelping pads, and many other things are routinely used in whelping boxes. I have tested all of them and more, and none provided adequate traction for every breed I tested or for the duration of the first few weeks of life as the puppy gains weight. 

How did I evaluate traction? I looked for the single give-away - extension and adduction of the back legs, looking like little puppies on popsicle sticks. If I saw pads facing the sky, the mat failed.

To be fair, I did find one mat that provided terrific traction. It was made from coconut fibers sticking straight up like broom bristles. It provided great traction, but it also took the delicate skin off the newborn puppy's foot pads. That too was considered a fail.

Here are some examples of what I observed watching puppies, and there are many similar examples to be seen in the volumes of puppy videos on YouTube if you care to browse (try searching on "newborn puppies nursing or crawling).

If you've been paying attention, you are probably wondering if the puppies in your whelping box ever reveal their rear foot pads because they're facing the sky instead of the ground. To give you some practice spotting the extended-adducted leg position (before you dash off to look at your photos!), check out these very busy puppies. At a casual glance, they look like they are getting around pretty well. But watch closely; these pups on this surface would fail the traction test.
​

I have made observations of hundreds of litters of puppies on all manner of surfaces, and so far the ONLY surface that provided adequate traction for all puppies (i.e., back legs were never fully extended and straight) was that coconut fiber mat that could take the skin right off the bottom of your feet. These are the mats you see inside large hotels in areas where it snows, so you can brush the snow off the bottom of your shoes with the bristles. They're designed to be harsh.

Now, this raises the obvious question. Is hip dysplasia the result of inadequate traction for newborn puppies in the whelping box? If it is, we could eliminate hip dysplasia now, simply by providing good traction that prevents slipping. It seems far-fetched, but if we haven't eliminated hip dysplasia after 60 years of strong selection, it's worth entertaining a new explanation.

​I've been working on solving this problem for the last few years. Finally, after fussing and fiddling with various types of surfaces, I have finally come up with one that prevents slipping and the damage to the teres ligament that can result in hip dysplasia. I am currently testing this surface on litters of various breeds of dogs, and so far it has worked well. I need to look at many more breeds and also observe the puppies over the first several weeks when their weight increases dramatically with growth. Of course, the acid test will be seeing if these puppies have sound hips, so some of these puppies will be scored at four months using PennHip, which quantifies hip laxity with the "distraction index." Will this ultimately solve the hip dysplasia problem in dogs? Time will tell. But I'm very optimistic.

​You can learn much more about hip dysplasia in ICB's online course, Understanding Hip and Elbow Dysplasia. 

By Carol Beuchat PhD

As we accumulate data from DNA testing, some interesting patterns are starting to emerge.

​A recent study has accumulated data for about 100,000 dogs, including about 83,000 mixed breed dogs and 18,000 purebred dogs representing 330 breeds (Donner et al 2018). For testing, the authors used a SNP array that tests for 152 known mutations, or "variants," at the same time. These tests cannot identify all mutations, only the ones that have been identified and localized at a particular SNP. So the data represent only a fraction of the actual number of mutations in the entire gene pool.

They organized their results in a Venn diagram, which identifies the number of mutations found in mixed breeds, purebreds, both, and not found in this population of dogs.

The data reveal that 34 mutations were only seen in mixed breed dogs, 13 were only seen in purebreds, and 25 were not found in this sample population. Of the mutations identified, 80 were found in both mixed and purebred dogs. If we add up the numbers for mixed and purebreds, we find that a total of 114 mutations (34 + 80) were found in mixed breed dogs, and 93 occurred in purebred dogs.

These results are very clear. More mutations were found in mixed breed dogs than in the purebreds. 

You might look at these data and conclude that this is proof that purebred dogs are healthier than mixed breeds. Would you be correct? 

Let's remember a few things. Recessive mutations are usually not expressed (i.e., they have no effect) unless the dog is homozygous for the mutation; i.e., to be affected, the dog must inherit two copies of the defective allele, one from each parent. A dog with only one copy of the mutation would be called a "carrier" and, for most recessive mutations, carriers suffer no ill effects.

One consequence of this behavior of recessive mutations is that a dog can be a carrier of many mutations but suffer no ill effects from any of them. In fact, because of this, recessive mutations can be passed from parent to offspring generation after generation without affecting the health of the dog.

Dogs that inherit two copies of a mutation (called homozygous, affected, or "at risk") are likely to display some negative effects like blindness, exercise collapse, a nervous disorder, or some other disturbance to a body function. If the consequences are severe enough, natural selection or the breeder will remove the dog from the population of breeding animals and those mutations are not passed on to offspring.

So we have two situations: in one, a dog carries a single copy of the mutation and suffers no ill effects (heterozygous), and in the other the dog carries two copies and the mutation is expressed as a genetic disorder.

Now look back at our Venn diagram. There are more mutations found in the population of mixed breed dogs. But what we need to know is whether they are homozygous and affect the dog, or heterozygous and are harmless.

This pair of graphs show the proportions of mixed breed and purebred dogs in which the mutations were heterozygous (left). The graph on the right shows the proportion of dogs in which the mutations were homozygous (right). Mutations in the heterozygous state on the left were found in both mixed and purebred dogs, but as we would expect from the Venn diagram above, more of the mixed breed dogs were carrying mutations (yellow arrow). The graph on the right shows what we really need to see: both mixed and purebred dogs had homozygous mutations, but they were much higher in purebred than mixed breed dogs.
​

​Here is what the study's authors had to say:

In a nutshell, here's what they found:

a) The collective population of mixed breed dogs contains more recessive mutations than that of purebreds, but those mutations are more likely to be heterozygous and therefore harmless.

b) On the other hand, there are fewer mutations found in purebred dogs, but they are far more likely to be homozygous, and therefore expressed as a genetic disorder, than in mixed breed dogs.

The fact that mixed breed dogs have so many mutations does not make them more prone to illness. In fact, they are less likely to be affected by a genetic disorder than purebred dogs, because the mutations are more often found in the harmless, heterozygous state. The mutation load in purebred dogs is smaller than in mixed breeds, but it is far more dangerous, because the mutations are much more often homozygous.

It is this simple property of recessive mutations, of only being expressed when homozygous, that results in the higher rate of genetic disorders in purebred than mixed breed dogs. 

This comparison of the health of mixed and purebred dogs is oft debated, and breeders usually argue that purebred dogs are just as healthy as mixed breed dogs. For problems caused by non-genetic disorders (broken bones, allergies, and the like), this could be true. But, for genetic disorders, the purebred dogs fare far worse than mixed breed dogs. It's a simple matter of the genetics of recessive mutations.

Why are there more mutations hanging around in the huge gene pool of mixed breed dogs? It's because recessive mutations are harmless if they are heterozygous, so they are not eliminated from the population by selection. The frequency of a specific mutations in the population is usually very low (< 1%, with a few notable exceptions, like the mutation associated with degenerative myelopathy, DM). The chances of any two random mixed breed dogs having the same mutations is low. Although a mixed breed dog can be affected by a genetic disorder caused by a recessive mutation if it inherits two copies, the chance of this happening is very low.

Breeding purebred dogs in a closed population means that all of the dogs in a breed are related and therefore share many genes in common. Some of these shared genes will be mutations. The more closely related the sire and dam, the more likely the puppies are to be afflicted with a genetic disorder caused by a recessive mutation.

This is why the best strategy for reducing the incidence of genetic disorders in purebred dogs is not endless DNA testing. To control the risk from all mutations, the ones you know about as well as the ones you don't, the best strategy is to reduce the relatedness of the parents. Reducing genetic disease in dogs boils down to reducing the risk of a puppy inheriting two copies of the same recessive mutation. The way to accomplish this is to reduce the relatedness of the parents. 

Mixed breed dogs have more mutations than purebreds. But they are less likely to be affected by genetic disorders because they are more likely to be heterozygous; i.e. have only one copy of the mutation.

REFERENCES

Donner J, H Anderson, S Davison, AM Hughes, and others. 2018. Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs. PLOS Genetics 14(4):31007361. https://doi.org/10.1371/journal.pgen.1007361

As breeders become more aware of the importance for genetic management to control potential genetic disorders, there are more and more discussions in groups about the best ways to do this. Little bits of information, packaged as what I think of as "pithy statements", are put forth as rules of thumb, and these are advocated as best practices. 

Somebody told me the other day that their group was thinking about making a rule prohibiting breedings that would produce COI > 10%, because they heard that 10% was the threshold of the "extinction vortex". She asked me if I thought this was a good idea.

This 10% extinction vortex statement is one of those pithy statements.

I advised her that breeders should NOT make a rule about this. Not because it's not true, but because "it's complicated."

Genetics can be complicated. The more you know about what's going on under the hood, the better decisions you will be able to make the next time you plan a litter. 

This would seem obvious, but in fact there are many nuggets of old "wisdom" that get passed around and around that are, well...not true. Yet, like a fly in the kitchen, it seems no amount of swatting at these untruths will get rid of them. 

Breeder! Unburden yourself of these myths! Embrace truth and science! Read on!

Common Breeder Myths
You've probably heard all of these. You've probably even repeated some of them. We will examine each of them. 
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Breed only BEST to BEST
Look, don't breed the dogs that have no good points. But, just like in school, realize that there can be a lot of merit in "above average". In fact, if the parents of a litter were quality dogs, then the offspring inherited quality genes, but perhaps not always in the best combination. Don't toss out those valuable genes - mixed a bit differently, they could produce the next superior animal. Remember: Improvement through selection requires genetic variation. Keep a good variety of ingredients in the genetic pantry to choose from!

Inbreeding is required to fix type
The genes for breed type should be fixed in the first few generations after breed formation. Once the breed has the qualities that define it, further inbreeding simply increases homozygosity in the other "dog" genes, for things like toenails and kidneys and glucose metabolism and saliva. If there are some mutations among the thousands of genes in the dog (and of course, there are!), then inbreeding will inadvertently produce paired (homozygous) mutations for some genes. For these, whatever the normal gene is supposed to do will be broken.

​Other domestic animals have clearly recognizable breeds with much lower levels of inbreeding than are typical in dogs. Most purebred dog breeds have average inbreeding in excess of 12%, and about half of the breeds are greater than 25%. In horses, most breeds are less than 12%.

Close the stud book to protect the breed
If the stud book is closed, genes will be lost from the gene pool through selective breeding and "genetic drift" (chance). If you start a breed with a founder gene pool, then lose genes every generation that cannot be replaced, eventually the gene pool will be depleted. You can easily test this with a bowl of M&M's on the coffee table. Grab a few when you need that chocolate fix, but don't put any back. Eventually, the bowl will be empty. 

The rule of thumb here: Animals in closed gene pools go extinct.

Really? Is this always true???

In fact, no. There is a very famous herd of cattle in England, the Chillingham cattle, that has survived for centuries as a closed gene pool. They are the iconic exception.

But every other closed population has gone extinct, and yours will too. You can count on it.

I know what's in my line
You probably know about dominant alleles. They mask the expression of recessive alleles. You cannot know what recessive alleles are lurking in your gene pool as long as expression is masked by a dominant allele. You could unmask recessives using inbreeding, because as we saw above, inbreeding breaks things. Or you could avoid inbreeding, not worry about the recessive lurkers, and keep that doggy working like a well-oiled machine.

Outcrossing introduces new diseases
Outcrossing does not "introduce new diseases". It introduces new alleles, some of which will probably be recessive mutations. But single mutations do not usually produce disease. In fact, as noted above, most recessive mutations are masked by dominant, normal-functioning alleles and produce no ill effects. Eliminate this problem by following a simple rule of genetic management: keep recessive mutations rare. So no popular sires! 

And remember from above: Inbreeding breaks things.

Hybrid vigor doesn't apply to dogs
Hybird vigor results when you "undo" inbreeding by mating two animals that are relatively unrelated. Inbreeding applies to dogs. So hybrid vigor applies to dogs. 

No, it hybrid vigor not require different species. In fact, most interspecific hybrids are infertile and not terribly vigorous.

Nothing will make you look dumber than declaring that hybrid vigor doesn't apply to dogs.

Do yourself a favor. Look this one up. So you never forget.

If you're a dog breeder and you believe in genetics (of course you believe in genetics!), you know that there is a certain predictability in breeding that is the result of genes being passed from parent to offspring. You take advantage of your understanding of the process of inheritance when you breed for certain colors, or you use a taller sire to put a bit more leg under your next litter. 

On the other hand, as most breeders will tell you, "breeding is a crap shoot". You are trying to breed for one a particular trait in your puppies and get instead a litter of puppies with something else or, even worse, a mish-mash of variety that beggars your belief in genetics.

Of course, the problem here isn't that understanding genetics is worthless. It's that you are trying to select a breeding pair based on the genes you would like them to pass on to their offspring. You are trying to select for particular genes, but you are assessing the genetic merit of a dog for a particular trait based on its phenotype - how those genes are expressed in a dog. This method of selection - evaluation of phenotype - only works well if phenotype is a good indication of genotype. As anybody who has ever bred a litter of dogs knows, for some traits phenotype is a good indication of genotype, and for other traits it isn't.

The most important concept in selective breeding is "heritability". If you ask 10 breeders to define heritability, I can almost guarantee that most will get it wrong. Most people will define heritability as the inheritance of a particular trait by a dog.

​But actually, heritability is a concept from population genetics. Heritability tells you how much of the variation in a trait in a group of dogs is the result of differences among them in their genes.

Now, let's say we could create an exact clone of each of those puppies and raise that duplicate litter separately. Each puppy goes to a different home, is fed differently, exercised differently, and raised under conditions that are unique to that puppy. Now when you measure the weight of each puppy at 1 month, you will probably get different numbers compared to each pup's clone, and there will probably be more variation in the litter. The pups have exactly the same genes, but ended up at 1 month with different phenotypes. We know that genes are important to weight, but in this case there are clearly effects of environment.

Here is where most people get tripped up on the definition of heritability. In the first example, the heritability of weight will be equal to 1. In the second example, the heritability of weight will be less than one, perhaps something like 0.3. Same trait, different heritabilities. Why? Because heritability is not about a particular trait in an individual, but rather tells us about the trait in a population of dogs. Here's why.

The phenotype of most traits depends on both genes and environment. We could write this in shorthand as

So for our example of weight in puppies above, the puppies in first litter were raised in identical environments, so the "E" term in our little equation is 0; there is no effect of environment on puppy weight, and all the variation you see among the puppies is due to genetics. So for these puppies, the heritability of weight is 100%.

I don't want to get into the details of heritability and how it is determined (these are things we discuss in the ICB courses). Rather, I want to make a simple but extremely important point. 

When you assess particular breeding combinations, you use whatever information you have about phenotype of the parents or relatives to make assumptions (or guesses, really) about the genes each parent is likely to pass on to each puppy. If the heritability of weight at 1 one month is 1.0, as for the first litter, you know that 100% of the variation in weight from pup to pup is due entirely to genetics. If you wanted smaller size in your next litter, you should keep one of the smaller puppies to breed and you should also get the genes for smaller size.

But what about the second litter, for which heritability of weight was only 30% because there was lots of variation in how they were raised? If you want smaller pups in your next litter, you can't assume that you are correctly selecting the genes you want for size just by the weight of the puppies. Some pups might have had more to eat, some might have been couch potatoes and put on some puppy fat, some might have been slow eaters and never got as much to eat as the others. In this case, phenotype is not a very good indication of genotype; there is lots of variation in phenotype because the "E" term in that simple equation above is not zero.

Okay, here's the rub. For most of the traits you want to select for (or against), there will be multiple genes involved as well as non-genetic factors that will affect phenotype. If you select the pick of the litter based on phenotype alone, you will not necessarily be selecting the puppy with the best genes for that trait. For puppy weight with a heritability (in our example) of 0.3 (30%), most of the variation in phenotype (70%) is because of things that have nothing to do with genetics. If your strategy for selection relies heavily on the phenotype of the dog, you are more likely to be wrong than right. 

If you don't know the heritability of a trait you are trying to select for or against, you are likely to make a lot of incorrect decisions based on phenotype alone. If you're assuming the heritability of a trait is 1.0 - i.e., what you see is what you get - you are going to have a lot of those "breeding-is-a-crap-shoot" experiences, selecting for one thing and getting something else. On the other hand, if you know that the heritability of a trait in dogs raised in uncontrolled conditions (different households, various diets, variable amounts of exercise) is 0.15, then you should understand that phenotype is not a very good reflection of the genes for that trait in an individual puppy and that you will not be very good at selecting the puppies with the genes you want. On the other hand, if the heritability of trait is typically 0.8, then phenotype will be a decent reflection of the genes for that trait inherited by that dog.

The critical point here is that heritability tells you how much of the variation in a trait is due to variation in genetics. If heritability is low, efficient selection will be difficult because phenotype is a poor reflection of genotype. If heritability is high, more of the variation in the trait among individuals is a result of genetics, so selection based on phenotype will be more effective.

There are ways to get around the limitations of selection when heritability is low. One is to use information about the relatives of a particular dog. If the heritability of hip dysplasia in a breed is usually about 0.2, and you found a sire you like but his hip score is mediocre, have a look at the hip scores of his litter mates, his parents, and, if he has already been bred, his own offspring. All of this information will provide clues about the genotype of that sire you like. If his relatives have good hips and he is the outlier, you can have more confidence that he probably has good genes, but perhaps he had an unfortunate experience as a puppy or was overindulged by an owner who fattened him up by rewarding everything he did with a cookie. You can do this assessment statistically using something called "estimated breeding values" (EBVs), which does some fancy math and comes up with a number that tells you about the quality of genes in a dog for a particular trait. (Some kennel clubs now provide EBVs for hip dysplasia.)

Hate that "crap shoot" part of breeding? You can reduce the guesswork in breeding by understanding heritability. Know the typical heritability of the trait you are selecting for, and take that into consideration when you evaluate phenotype. And also make use of information available from the ancestors, siblings, and descendants of a dog, because those animals share many genes and can help you decide how much weight to put on your assessment of phenotype when you are trying to select for particular genes.

Breeding will always have an element of chance, because that's how genes are inherited. But it doesn't have to be a crap shoot. Understanding how to use some simple tools like heritability can help you make better decisions and result in more predictability and consistency in your puppies.

To learn more about the genetics of dogs, check out
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Breeding strategies should not be ideologies. They are the means to achieve a genetic end, and the savvy breeder will use them appropriately. Breeds with small gene pools that can no longer produce healthy dogs have to use breeding strategies to fix that problem, and in many cases cross-breeding is be necessary. This is the case with the Norwegian Lundehund, a breed on the brink of extinction that is bouncing back thanks to a scientifically managed cross-breeding program. There are other genetic rehabilitation projects ongoing that involve cross-breeding, all under the guidance of scientists with appropriate expertise. Cross-breeding is not a philosophy. It is a breeding strategy, and one I would point out was used routinely by "purebred" dog breeders 100 years ago because they understood that a strictly closed gene pool was unsustainable. They didn't do it because they were "pro" crossbreeding; they did it because it prevented the deterioration in health of their animals that resulted from too much inbreeding. Modern dog breeders have forgotten that lesson, and the long list of genetic disorders in dogs is the predictable result.

I do not have a "personal stance" about any aspect of dog breeding. I am not a dog breeder; I have no opinion about how to do it. I understand the science of breeding and the role of population genetics in determining the health of the gene pool and the population of animals. Everything I say is based on facts.

This isn't the first time somebody has rushed around fear-mongering about me. I am happy to tell you completely, clearly, exactly who I am and what I am doing. My "alignment" is to science, and to the professional scientists whose expertise and research is essential to understand how we can improve the breeding of dogs. I communicate with them, I collaborate with them, and I respect them. I get my information from them and the army of other scientists that are working towards improving the health of dogs, not from people on Facebook with opinions and no expertise. I suggest you do the same.

As a final note:
The International Partnership For Dogs (IPFD) is an organization of kennel clubs, canine health organizations, scientists, genetic testing organizations, and others involved in improving the health of dogs. They met just a few weeks ago in the UK to discuss issues affecting the health of purebred dogs. The producer of Pedigree Dogs Exposed was there, as she was for all of the previous meetings of IPFD. A committee was formed to address issues of genetic diversity in dogs, and she was placed on that committee. She has the respect of the people at that meeting, and if they respect her, so do I.

So stop the fear-mongering. Do your homework. Read the science. Learn something. Align yourself with the people that have the passion and expertise to do right by dogs and are working towards better health based on science.