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

One of the problems with strong selection in a closed gene pool is that the dogs become progressively more and more similar genetically. Although selective breeding in purebred dogs results in consistency, it also has the downside that a breed can find itself stuck in a genetic cul-de-sac from which it can't escape. If you need to change the direction of selection, for example to breed towards a different trait or away from a genetic disorder, you need to find dogs with the genetic diversity necessary to support selection in a different direction. Genetic diversity is the raw material for selection; you can't change anything without it.

How much genetic diversity is there in your breed? How can you find the dogs that might have the genetic variation that you're looking for?
​

There are several different ways to determine how much genetic diversity there is in your breed, but let's look at one that uses the kinship coefficients that we have already been talking about (see Parts 1, 2, and 3 in this series; links at the bottom).

Let's say that we have a population of animals that are not closely. If we compare the genes in each dog with those in every other dog in the population, we can compute each dog's mean kinship, which I explained in a previous post. Since we know the dogs in our population are relatively unrelated, we know that the values for mean kinship will be low (they can range from 0 to 1). If we graph the mean kinship of all of the dogs in the population, we might get a chart that looks like the first one on the left below for Labrador Retrievers, in which all of the values are less than about 0.06. On the other hand, if we have a population of closely related dogs, we might get a graph like the last one on the right below for Irish Wolfhounds, in which most of the values are greater than 0.3. If you scan the graphs for the other breeds depicted below, you will see that the distribution of values for mean kinship can vary considerably.

What do these graphs tell us about genetic diversity?

Remember that mean kinship is the average relatedness of a dog to all others in the population. The Labrador Retriever is one of the most popular breeds in the world so numbers are very high, and there are populations of show dogs, hunting dogs, personal pets that will all be a bit different from each other genetically, and populations in different countries will probably be different from each other as well. This is a breed with a LOT of genetic diversity, and the mean kinship values are mostly low. But if you were to make another graph with just the show dogs, the distribution would probably be skewed towards higher values because those dogs would be more closely related to each other than they are to field line dogs.

When you compare Labradors with Irish Wolfhounds, the graph is skewed strongly towards much higher values. This indicates in this population of over 200 dogs, the average relatedness was very high. The exception is a few dogs that fall far below the pack and are not closely related to the bulk of the population. This indicates that most of the dogs are closely related to each other.

Because the kinship coefficient is based on genes that are the same because they are inherited from the same ancestors, we can interpret these graphs in terms of relatedness. If you breed two first cousins from parents that are not inbred, the predicted inbreeding coefficient of their offspring is 0.0625, or 6.25%. Looking at the graph at the top for Labrador Retrievers, we can see that most of the values of mean kinship are lower than 0.06. So we can say for this population that on average, the Labradors are less related than first cousins. 

You can do the same thing for the graphs for other breeds, using this chart for the kinship coefficients for each level of relatedness.
​

So, looking at the chart for Irish Wolfhounds (bottom right), you can see that most of the dogs have a mean kinship > 0.25; that is, on average most of these dogs are more closely related to each other than full siblings. Imagine a family reunion with a few aunts, uncles, and cousins, and 134 of your siblings. This is a breed with a very high level of average relatedness to each other. Likewise for Cavalier King Charles Spaniels. In the small sample of Havanese, there two clusters of dogs, one with a relatively high level of relatedness to each other, and another with rather low relatedness. 

There are several different ways to understand the genetic diversity in your breed. Here, we show you how you can use the kinship coefficient to provide information about the average levels of relatedness in a population of dogs. This is another tool you can add to your genetic toolbox!

About 80% of the genetics diseases we know about in dogs are caused by a single recessive mutation. Using modern DNA technology that enables us to scan thousands or millions of markers in a dog's genome, we can usually find these broken alleles and develop a test that breeders can use to screen their dogs.

Many disorders, however, are not the result of a single mutation. For these, there might be dozens or even hundreds of genes involved. Creation of a test that will identify an affected dog with no symptoms, one likely to produce affected offspring, is not likely to happen for most of these. This is a huge problem for breeders, because many of these diseases, like cancer, epilepsy, autoimmune dysfunction are very serious and becoming more and more common. Yet they do seem to run in related dogs, so we know genetics is important. How can we manage these diseases if we don't have a DNA test? We can use kinship coefficients. Watch this.

Kinship coefficients provide information about the relatedness of dogs by assessing pairwise genetic similarity. A statistical technique called cluster analysis can use the kinship data to construct a dendrogram - a genomic pedigree - that groups dogs together that are closely related and also indicates the relationships among groups. If a trait or disease has a genetic component, we should expect that clusters of closely related dogs are more likely to share traits than unrelated dogs because they share many of the same genes. ​

​This is a dendrogram constructed using kinship coefficients computed from DNA data for 211 Irish Wolfhounds. The upper figure is the right to the right blown up so you can see a bit easier, and the lower chart is the entire dendrogram. 

Let's take a little tour of the lower chart. You can see that the population of dogs has been separated into two smaller groups at the arrow labeled "A". If we follow the branch that comes off point A to the right, we come to a second branch at the arrow B that creates two subgroups. If we follow that branch at B to the left, we come to branch C that again splits the dogs into two groups. You can see now that is called a dendrogram because it is a picture of a structure that branches like a tree.

Dendrograms are a bit tricky to read properly and getting good at it takes some practice. You need to remember that branches can rotate around any branching point. So for instance, the very top branch that divides at A can be rotated around the junction at A so that the green group on the far left is moved to the far right to sit nest to the turquoise group. Clearly, that green group is not most closely related to the red group that was right next to it at when it was at the left end of the chart. For that matter, we can rotate the two groups on the far right (at arrow D) so  the green group is now right next to the red group. So there are actually many different ways to arrange the clusters that don't change their relationships to each other. This is because relatedness is indicated by the length of the lines that connect groups or dogs. Dogs connected by very short lines are closely related, and dogs that are more distantly related are connected by longer lines. When we swivel groups around branching points, the length of the connecting lines is not changed so the information about relatedness is not changed. (Check out How to read a dendrogram)

Now we have a picture of the genetic relationships among all of the 211 dogs in this sample. We also have information about which of these dogs has been diagnosed with epilepsy. This is indicated by the three asterisks ("***") at the tip of the branch for each dog. For dogs without asterisks, this could be because they have never reported epilepsy or we have no information. So this chart can't be taken as a representation of which dogs have epilepsy and which do not. It only tells us which dogs have reported a diagnosis of epilepsy.

So, what does this graph tell us? We can see that affected dogs tend to cluster together by family groups, which likely reflects a genetic component to disease risk. Unfortunately, there are no large groups where epilepsy is completely absent. This tells you that the genetic predisposition to epilepsy is widely, but possibly not uniformly,  distributed throughout this population of dogs. With some good record-keeping and the addition of data to the database, we might be able to come up with a clearer picture of the patterns of risk that can be used to make breeding choices that will reduce the number of affected dogs.

There are many breeds battling to control genetic disorders for which there are no DNA tests, or the test is unreliable for identifying dogs that will develop the disease (e.g., degenerative myelopathy). For these, kinship analysis could provide very useful information to breeders about risk of disease. Of course, the same technique described here could also be used for diseases caused by single mutations. If incidence of all genetic disorders was mapped on a dendrogram and kept up to date, breeders could notice a problem developing long before it becomes widespread in the breed and difficult to manage because of the high frequency of carriers. 

One caveat about dendrograms from kinship coefficients. The cluster analysis uses the information for all dogs in a sample population to construct a tree that is most likely to reflect their true relationship. If more dogs are added to the population, the groups might be sorted differently because the relationships among them are changed. So to be useful, data for kinship should be updated regularly and needs to accurately represent the genetic breadth of the population of interest. This would be true 

We can produce kinship coefficient from both pedigree and DNA databases. There is some advantage to the DNA data because it will distinguish differences in relatedness among siblings whereas pedigree data does not. On the other hand, the pedigree information is invaluable because it doesn't require collecting a DNA sample and the cost of analysis. If you aren't trying to compare siblings, you need to run only one or maybe two dogs in a litter, which can reduce the expense considerably.
​

Think about the valuable information analysis of kinship coefficients could provide to inform your breeding decisions and managing the genetic diversity of the breed. If you have a pedigree database or genotype analysis from high density SNPs, it would be well worth doing.
​

By Carol Beuchat PhD

This is part 2 of "Cool tricks with kinship coefficients". Check out "Part 1: Is this dog really an outcross?"

One of the major ways genetic diversity is lost from a breed is through selection. In wild animal populations, most animals produce offspring and pass their genes to a new generation. The progeny that inherit the best combinations of genes survive and reproduce themselves, and those that were not as lucky are culled by natural selection. 

In dogs, we often breed only one or two puppies from a litter, selecting those that we feel best suit the goals of the breeder and are good representatives of the breed. But if you started with a sire and dam that you felt were quality dogs, all of those puppies should have "quality" genes but in different combinations, some of which make for a "better" puppy than others. When the pups judged to be less suitable are not bred, we risk losing from the gene pool some of the genes that produced the good quality in the parents. We limit our future breeding options when we lose those genes, and we also remove the opportunity of tossing them together with a mix of genes from another parent dog to perhaps produce something wonderful. You can't breed every dog, and not every dog is worth breeding.

If you breed for both quality (on whatever scale) and health (and of course you so), you should be concerned about the inadvertent loss of genetic diversity that results from selective breeding because eroding the genetic base of the breed will have consequences down the line. But how do you determine which dogs are important for preserving genetic diversity? You can use the kinship coefficient.

The kinship coefficient (K) is an estimate of the genetic similarity of two animals that are related by ancestry. As I explained in Part 1 of this series (Cool tricks with kinship coefficients, part 1: Is this dog really an outcross?), the kinship coefficient of the sire and dam determines the inbreeding coefficient of their litter. Put another way, the inbreeding coefficient of a dog is the kinship coefficient of its parents. (And remember from part 1 that K must always be a comparison of two individuals.) We are going to see how you can use the kinship coefficient to assess the genetic value of a dog to the breed.

Below is the same kinship matrix we talked about in my previous post about kinship coefficients. Again, the white squares on the diagonal are each dog compared to itself (so K = 1), and the other squares are color-
​coded to make it easy to spot combinations that are less (or more) related to each other.

We can use the color coding indicated in the three squares in the upper left corner on the matrix to easily spot dogs that are closely related to other dogs (i.e., green, yellow, and red). If you follow across the rows of dogs 6 and 7 from left to right (or follow down the columns for these two dogs if you prefer), you will see that there are lots of red, orange, and yellow squares, indicating dogs as closely related to 6 and 7 as half-siblings (K = 0.125) to full siblings (K = 0.25). This means that the genes in dogs 6 and 7 are also found in other dogs in the population because they share ancestry.

Now do the same thing for dogs 3 and 4. You will find that most of the squares are green, indicating that they are not closely related to most of the dogs in this group. Interestingly, 3 is as related as a full sibling to 9 and 10 (K = 0.25), which are likewise closely related to each other; similarly, 4 is closely related to 11 and 12, which are likewise  as related as full siblings. It would be interesting to look at the genealogical relationships among these four dogs from pedigrees. 

If dogs 6 and 7 have many relatives in the population and dogs 3 and 4 have very few, then the latter pair are genetically more valuable because they carry genes that are not common among these dogs. It is fairly easy to identify the genetically important dogs in this small example population, but how can we do it with a large population of dogs with complicated patterns of relationship?

The easiest way is by computing the mean (average) of all of the kinship coefficients for each animal. In the figure below, have added a column on the right labeled mK, for "mean kinship". It is easily computed by adding up all the values in a row and dividing by the number of dogs. (The kinship coefficient of each dog with itself is included in the calculation.) Now we have a column of numbers in which it is easy to see which dogs, by the bright yellow squares, are most genetically different from the rest. Although on average, they are as related as half-siblings to the rest of the population, we know that it includes dogs with little or no relatedness, and you should keep this in mind when you are comparing the values for different dogs. It is always worth examining the kinship matrix to see whether a dog with K = 0.125 is closely related to everybody, or instead is unrelated to most of the dogs but closely related to a few that drive up the average (as here).
​

Now we can use the data for mean kinship to quickly identify the dogs that are genetically most valuable in a large population.  The simple bar graph organizes the dogs by rank, with the lowest values of K to the left - the dogs with the highest genetic value - and high values to the right (the dogs with lowest genetic value). In this population, there are a few dogs with high genetic value, but most of the rest of the population is closely related.

We should be using kinship coefficients much more than we are, and that is to the detriment of maintaining genetic diversity in our breeds. Breeders should know which dogs are genetically valuable, even if they aren't the top winners in competition, because the genetic variation they carry is the raw material for breed improvement in the future. Lines lost are lost forever. Perhaps breed clubs should have a genetic diversity committee that is responsible for monitoring the population to prevent loss of variation, or this could fall to the health committee because diversity and health go hand in hand. Note that if everybody rushes to breed to the least related dogs, their genes will become common and intermixed in a way that prevents them from being used strategically to manage genetic diversity. Diversity should be exploited strategically. (For the same reason, there should be a "popular sire" monitor, whose job it is to keep an eye out for sires producing more than their fair share of puppies.)

Learn how to use the kinship coefficient to take some of the guesswork out of decisions about genetic relatedness or uniqueness when you are considering your future breeding plans. This simple tool can provide you with a wealth of valuable information!

Learn how you can use kinship coefficients in
​this terrific new ICB course!
​

To learn more about the genetics of dogs, check out
ICB's online courses

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By Carol Beuchat PhD
​

Every few generations, it's a good idea to cross out to a relatively unrelated dog to bring in some new genetic diversity and freshen up your lines. But finding the right dog to do this with can be tricky. A dog that doesn't share any ancestors with the dog you want to breed in the last 5 or 6 generations might have enough shared ancestors farther back in the pedigree to provide a lot of relatedness. Or even worse, maybe you don't have a decent pedigree database so you really have no idea how closely two dogs might be related. This is an especially irksome problem if you're contemplating bringing in an expensive import. You really don't want to get it wrong. 

So what do you do? How can you identify a dog that will be a good outcross for your breeding program?
​

The kinship coefficient is related to the coefficient of inbreeding: the coefficient of inbreeding of a dog is the kinship coefficient of its parents. So, the kinship coefficient between a potential sire and dam is also the predicted inbreeding coefficient of their litter. The kinship coefficient in population genetics uses the Greek symbol phi, as in this figure.
​

The kinship coefficient can be calculated from a pedigree database, just as inbreeding coefficients are. But it can also be estimated directly from DNA data - in effect, the "realized" kinship coefficient that reflects the actual level of shared ancestry between two dogs based on their DNA.
​​

Let's look at this very simple pedigree containing 14 dogs. Perhaps you were contemplating doing a breeding between dogs 14 and 7, but you are worried that it might be too close. You want to know how closely related - genetically similar - those two dog are. The kinship coefficient will tell you this. Here's how.
​

The kinship coefficient is always a comparison of two dogs. You can compute the K for each pair of the dogs in the pedigree and display them in the form of a matrix. Each dog is listed down the side and also across the top. The number in the box where the column and row of a pair of dogs intersects is the kinship coefficient of that pair. The white boxes on the diagonal are each dog compared with itself.
 

For example, we can determine that the kinship coefficient between dog 14 and dog 7 is 0.19, or 19%. This means that if you were to choose one allele at random from the pair of alleles at a particular locus on the DNA of dog 14, and likewise choose an allele at random from that locus for dog 7, the probability of choosing two alleles that are identical because they were inherited from a common ancestor is 0.19, or 19%. To put it another way, the chance that the offspring of this pair of dogs will be homozygous at that allele (have two identical copies of an allele inherited from a common ancestor) is 19%. Furthermore, if these two dogs were to produce a litter, the predicted coefficient of the puppies would average 19%.

Computed from a pedigree, the kinship coefficient is an estimate of the average expected kinship coefficient; that is, the shared genetic relatedness because of shared ancestry. But kinship can also be determined directly from DNA genotyping data, such as is provided by Embark. (As far as I know, this is the only company that will allow dog owners to download the raw data for their dogs.) When based on DNA, these are "realized" rather than predicted estimates of genetic relatedness, and they will be different for every dog in a litter.
​

Now, here's the beauty of this. Let's say you're looking for a dog that will be an outcross for a bitch you want to breed, and you're willing to import a dog if you have to. You have computed the kinship coefficients from the pedigree database available for your breed, and there are two dogs overseas - litter mates, in fact - that look promising. Would these dogs be a good outcross for your bitch? Would one of these be a better genetic fit to the bitch than the other?

To answer these questions, you can do direct comparisons of the genomes of these two dogs with the bitch you want to breed by calculating the kinship coefficient for both of the sire-dam pairs. Modern DNA analysis using "single nucleotide polymorphisms" (SNPs) can now provide excellent data with very high resolution that you can use to do this. ("Single nucleotide polymorphism" is a fancy term for loci that are highly variable ("polymorphic"); the abbreviation is pronounced "snips".) We can easily and inexpensively compare hundreds of thousands - even millions - of loci on the chromosomes of a pair of dogs, assess whether the alleles at each of those loci are the same or different. Further, using data for allele frequencies in the larger population we can determine if the shared SNPs are copies of the same allele in a common ancestor; that is, they are "identical by descent" (IBD). This is the technique used for establishing the relationships among many breeds of dogs (Dreger et al 2016), and it is also used to identify genetic mutations associated with diseases in genome-wide-association studies (GWAS).

Instead of estimating kinship from a pedigree database, which will only give you one number that applies to the entire litter, you can estimate the actual degree of genetic similarity between two dogs. In fact, using SNPs you can even see which areas on each chromosome are shared. You can use this information to see if blocks of homozygosity overlap in two dogs, in which case all of the offspring would also be homozygous in the same place. (More on this in an upcoming blog post!) You can specifically look at characteristics of the genome of the two litter mates and determine if there are any ways one might be a better match to your bitch than another. And the kinship coefficient will also tell you the estimated inbreeding coefficient of the litter produced by each potential sire. 

For the preservation breeder, the genomic kinship coefficient from SNP genotype data provides you with the best, most advanced tool available today for genetic management to improve the quality of your puppies while also protecting genetic diversity for the health of your breed in the future. 

We will be learning about kinship coefficients and how to use the kinship matrix in ICB's new course, "Strategies for Preservation Breeding", which starts 10 September 2018. Join other preservation breeders who will be using this powerful tool to improve their breeding program. If you're interested in using genomic kinship coefficients to explore options for your next breeding, contact ICB and we will work with you to set that up. 

Watch this space for more Cool Things you can do with kinship coefficients!

REFERENCES

Dreger, DL, M. Rimbault, BW Davis, A Bhatnagar, HG Parker, & EA Ostrander. 2016. Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic trait mapping. Disease Models and Mechanisms 9: 1445-1460. (pdf)

Hayward, JL, MG Castelhano, KC Olivera, and others. 2016. Complex disease and phenotype mapping in the domestic dog. Nature Communications 7:10460. DOI: 10.1038/ncomms10460. (pdf)

Li, M-H, I Stranden, T Tiirikka, M-J SevonAimonen, & J Kantanen. 2011. A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population. PLoS ONE: Nov 2011; Vol 6:11. e26256. (pdf)

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Most of the genetic disorders in dogs are caused by recessive mutations, a single broken allele. There are now tests for dozens of disorders that can detect whether a dog has inherited one or two copies of the broken version of an allele. With the DNA testing information, we can reduce or eliminate the risk of producing puppies that will be born with a disease caused by one of these recessive mutation.

Draw a square and divide it in half both ways to produce four compartments. Each compartment will represent a puppy (or a pea seedling, or whatever). Above each of the columns, note the genotype of the father for the gene in question, indicating the dominant allele with an upper case letter and the recessive version with lower case. On the left side, label the rows with the alleles present in the mother. In this example, the father is heterozygous for the B gene (Bb) and the mother is homozygous recessive (bb).
​

​

​Now, to see what we do next, click on this little alien that can't wait to show you the basics -
​

The Punnett square works just as well for predictions of two traits at a time. Here's an example of a "dihybrid" cross involving two genes in guinea pigs, one for coat color and the other for coat length. The Punnett square makes it easy to map out all 16 possible combinations of inheritance in just a minute or two.
​

Have a go at checking the red, blue, and greed Ridgebacks and see if you get the same results for each pair of parents on the left. And below are some other examples you can play with. By the time you've worked through these, you'll be a pro!

I was honored to be asked to do a presentation about the genetics of the Afghan Hound at their World Congress, which was held in August 2018 in Amsterdam. This is a summary of the information presented.

This is also a great example of the amount of useful information that can be extracted from a basic pedigree database. Using tools from population genetics, we can explore the genetic history of the breed from the founders up to the present day. Along the way, we can examine the genetic impact of each of the founders, the consequences of popular sires and bottlenecks, the effects of historical events such as wars, and changes in breed popularity that affected population size. We can see how genetic diversity has been lost over the generations, and determine the current size of the gene pool and the effective ("genetic") population size.

That's a lot of great info and also a good example of how population genetics can help breeders more effectively manage the genetic health of their breed.

Even if the Afghan Hound is not your breed, this should be interesting to you. And if your breed has a pedigree database, it's worth going through this to see some of the amazing things you might be able to learn about the genetic history and present status of your own breed!

 In the breed’s first decade, the Bell-Murray dogs dominated the gene pool. By 1929, four B-M dogs accounted for 59% of the gene pool, each contributing more than 10% to the total genetic variation.

In the breed’s second decade, the influence of the B-M founder dogs diminished. The founder dog with the single largest genetic influence was Sirdar of Ghazni, whose contribution to the gene pool amounted to nearly 30%. No other founder dog from either kennel contributed more than 10% to the gene pool.​

(Offspring of first generation founder dogs also appear on this chart.)

This graph covers the same period of time as the previous one and displays the percentage of dogs born that produced offspring.

After the early years of breed foundation, the fraction of dogs bred has varied from about 15-50%. There is a peak in 1965 that corresponds to the start of the period of exponential growth. However, while the population was exploding, the fraction of dogs being bred actually declined and didn’t stabilize until about 1975, which corresponds roughly to the peak in the number of dogs produced per year.​

Since 1990, the fraction of dogs that produce offspring has been declining from about 25%, and it appears to be dropping rapidly in the last decade. The most recent estimate (for 2013) is only 7%.

Shirkhan of Grandeur came just as the popularity of Afghan Hounds was increasing in the 1960s, so although he was not an especially prolific sire, his descendants contributed significantly to the increase in numbers during that time. ​

The graph on the left shows the number of offspring he produced from 1956 to 1968. The graph on the right is the cumulative number of his descendants over the next dozen generations. After 10 generations, he had > 130,000 descendants. The total number of dogs in the pedigree database between 1955 and 2017 is 197,214.

Historically, purebred dogs have had closed stud books; every dog must be from registered parents, and all dogs in the registry go back to the same (few) founder dogs. The exceptions would be dogs from outside the breed that are specifically approved to be registered.
​
Because every dog must have registered parents and all share the same founders, ALL breeding of purebred dogs is to related dogs. This is the definition of “inbreeding”. Breeding related dogs creates homozygosity because related dogs share some of the same genes. Homozygosity refers to the inheritance from an ancestor of the same allele from  both parents. There can be close inbreeding (e.g., siblings) or distant inbreeding (third cousins), but it’s all inbreeding - it produces homozygosity.

There are advantages and disadvantages to inbreeding. Inbreeding reduces variation among animals and increases predictability in breeding. It also increases prepotency, so parents produce offspring that share their traits.

​But there are also significant disadvantages to inbreeding, mostly related to health. Inbred animals are less fertile and produce fewer offspring, and they are more likely to express diseases caused by recessive mutations.
Because the disadvantages of inbreeding affect the success of your breeding program, we tend to worry a lot about inbreeding.

When the small number of founder dogs for a breed is low, there is no way to avoid early inbreeding.

This chart contains the inbreeding coefficient of every dog in the pedigree database for which one can be calculated. The very low or zero values that you see represent dogs with missing ancestors or parents; these values will be underestimates of actual inbreeding so they are an artifact of the data.​

You can see that over the history of the breed, most dogs have inbreeding coefficients higher than 0.05, or 5%. Most dogs fall in the range of 10-30% (0.1 to 0.3).

This is the same graph you just saw. I have added some colored lines for particular levels of inbreeding.

The lines are for inbreeding that would result from crossing full sibs (25%; red), half sibs (12.5%; yellow), and first cousins (6.25%; green). (These assume the parents in each case are not inbred; otherwise these values will be higher.)​

This graph is similar to the one you just looked at for inbreeding, except it is for something called the “kinship coefficient”.

The kinship coefficient (K) is an index of the relatedness (or genetic similarity) of two animals. It is always a comparison of two individuals. The kinship coefficient is related to the inbreeding coefficient: the inbreeding coefficient of a dog is equal to the kinship coefficient of its parents. Similarly, the kinship coefficient of two dogs is the average inbreeding coefficient of their offspring.

We can use the average (mean) kinship coefficient of the animals in a population (mK) to assess how closely related they are to each other. If the mean kinship coefficient is high, then the dogs are, on average, very similar to each other genetically; if the mean kinship coefficient is low, then on average the dogs are less similar genetically.

The graph shows the distribution of mean kinship values that would result if the current population of Afghan Hounds was breeding randomly.​

(Remember that just as for the inbreeding coefficient, missing data will underestimate this value.)

These are the graphs you just saw - of inbreeding coefficients on the left, and mean kinship coefficients on the right.

We can learn something about the breeding strategies being used in a population by comparing the data in these two graphs.

Looking at the graph on the right, we can see that if Afghan hounds were breeding randomly, mean kinship coefficients would be relatively low, ranging from 10% to 15%.

From the graph on the left for inbreeding coefficient, we can see that while many dogs fall in the range of 10-15%, most are higher than this. ​

When the inbreeding coefficient is higher than mean kinship, this indicates that breeders are preferentially mating dogs that are more closely related to each other than the average relatedness in the population. That is, even though most of the dogs in this population are already more closely related than half-sibslings, breeders are still choosing mates that are even more closely related than this.​

This also means that with proper mate selection, breeders could reduce the level of inbreeding in their litters by choosing pairs with a lower kinship coefficient.

We are always hearing about the high level of inbreeding in dogs. How high - or low - is inbreeding in dogs? 

This chart shows the average inbreeding coefficient of a large sample of dog breeds based on DNA data instead of pedigrees. The breed names are probably too small to read, but the Afghan Hound is indicated by the arrow. The inbreeding levels are marked by horizontal lines as before, with red (25%) for a full sib cross, yellow (12.5%) for a half-sib cross, and green (6.25%) for a cross of first cousins.

The average inbreeding coefficient of the Afghan Hound estimated from DNA analysis is about 30%. This is about the “middle of the pack” for the breeds that have been studied.​

This compares to about 20% based on pedigree data. Remember, however, that incomplete pedigree data will underestimate actual inbreeding.

Is 20% or 30% inbreeding “high”? We can compare dogs to other domestic animals.

The graph at the bottom is the one you just saw for dogs, with Afghan Hound marked with the arrow. The chart at the top is average inbreeding based on DNA for horse breeds, with the same colored lines to mark levels of inbreeding.

Only one breed, the Clydesdale, has an average inbreeding > 25%, and more than half of these breeds are less than 12.5%. In fact, about a dozen breeds average about 6% or less. ​

Inbreeding in purebred dogs is far higher than in horses, and indeed higher than is typical of other purebred domestic animals. Certainly it is the case that high inbreeding levels are not a requirement of either domestication or of maintaining the traits that make each breed unique.

This is a graph of how the size of the Afghan Hound gene pool has changed over time. The triangles along the x-axis indicate unrelated dogs (i.e., new “founders”) added to the population after 1925.

Just look at the blue line for now. This is the line for the “effective number of founders” (fe) - specifically, the number of unrelated dogs that would contain the same amount of genetic diversity as the actual population at a particular time. The highest value, fe = 16.5, occured while the breed is being founded.

By 1930, genetic diversity had declined to fa = 9.5. In another decade, fa is reduced and after that it averages about 9.

Additional unrelated dogs occasionally introduced through the 1970s prevented a reduction in the size of the gene pool.​

The size of the current gene pool is about 9.

Hank passes all of his health testing - eyes, hips, and the DNA tests available for the breed.

He produces dozens of lovely, healthy puppies. Many other potential sires are not used, and their contribution to the gene pool declines or might be lost completely.

Each puppy inherits half of its genes from its dam and half from Hank. By random chance, half of the puppies produced by Hank will carry one copy of his recessive mutation. They are not affected by it, because they inherited a normal copy of the gene from their dam.​

Everyone is thrilled with the stunning, healthy puppies sired by Hank.

Usually, it is forgotten that Hank’s mutation became a problem because he was a popular sire.

The next big winner will probably also become the next popular sire, and his unique mutation will be passed to dozens or even hundreds of puppies. The cycle will continue, and a new genetic disorder will probably be produced. ​

We can completely prevent genetic disorders caused by recessive mutations. Don’t create popular sires.

We noted earlier that genetic diversity is lost from the gene pool because of selection.

The other way diversity is lost from the gene pool is “just by chance” - called genetic drift.

Because genes are inherited randomly, not every gene in every parent will be copied into a puppy of the next generation. If an allele is rare in the breed, it can be lost entirely. The change in the composition of the gene pool from generation to generation just due to chance is called “genetic drift”.

Most breeders don’t worry at all about genetic drift. If breed populations were very large, the chance that a rare gene would be lost is low. However, if the population size is small, the loss of rare genes through genetic drift can be high. ​

For population size, it is not the total number of animals in the breed that matter, but just the ones that are breeding. As we have seen, the breeding population is usually only about 20% of the census population. And if those breeding animals are related, the “genetic size” of the population will be even smaller.

The “genetic size” of a population is called the “effective population size”, Ne.

Ne is the size of a hypothetical population that loses genetic diversity at the same rate as the real one of interest. There are many things that can affect Ne, but two important ones are 1) the number of animals bred and 2) the ratio of females to males, both of which we have discussed for Afghan Hounds.​

This graph is very similar to one you’ve seen before. But instead of actual number of animals on the y-axis, this one has the effective population size.

You should know the effective population size of your breed is because it is linked to the rate of inbreeding. As effective population size gets smaller, the rate of inbreeding increases exponentially.

The larger graph (which looks empty) shows how inbreeding (as % per generation) is affected by Ne on linear axes. You can see that for Ne greater than about 100, this line looks nearly flat. Below 100, however, it increases very quickly.

If we log both axes, this curve becomes linear. Now we see in the inset graph that when Ne is small, even a small change will have a large effect on the rate of inbreeding.

What is the message here for Afghan Hounds? As the number of breeding Afghan Hounds continues to decline, we can expect to see inbreeding increase.​

For Ne, how small is too small?

This is the graph of effective population size for Afghan Hounds over the years since the breed was founded. 

As a general rule of thumb, the effective population size should be about 500. This is considered the size for a sustainably breeding population because the rate of inbreeding will below and there will be low risk of extinction. The effective population size of the Afghan Hound fell below 500 in about 1995 and has declined slowly since. ​

We are only interested in the most recent decades for Afghan Hounds, so lets change the axes on the graph.

This is just the last few decades from the previous graph, from 1980 to the present.

There is a green line at Ne = 500 is as before. A yellow line has been added at Ne = 100, which is considered a minimum population size. 

And there is a red line at Ne = 50, which is considered to be the “emergency” value of Ne, below which a population is at risk of extinction from inbreeding depression and genetic disease.​

The effective population size of the breed is currently about 100 and will likely continue to decline. Breeders should act to reduce a further declines in Ne by increasing the fraction of dogs used for breeding. You can do this without increasing the number of puppies produced.

There is a growing list of genetic disorders known to afflict the Afghan Hound. 

A few of these might be caused by single mutations for which a test could be developed - e.g., progressive retinal atrophy, von Willebrand’s. But there are no DNA tests available for the Afghan Hound.​

Most of these are polygenic, so genetic management must be through breeding strategy.

A last word on GENETIC DISORDERS - We’re doing this all wrong!

Here’s the usual process. A disorder pops up in the breed (popular sire?). We spend money and time to study the disease, look for a gene, and develop a test. For a few problems, we find a gene. For most we do not. And new genetic disorders continue to appear. Dogs are not getting healthier.

We can solve the problem of genetic disorders in dogs faster and better than we are using proper genetic management. Low inbreeding will reduce risk of ALL disorders caused by recessive mutations. Minimize loss of genetic diversity so you don’t lose important genes. (They’re all important!) And avoid popular sires.​

Here’s an analogy -

The Afghan Hound faces several issues that potentially threaten its future.​

1) Falling popularity and therefore declining population size
2) Inbreeding
3) Small gene pool
4) Popular sires
5) Genetic disorders
​

How can breeders address the issues faced by the Afghan Hound?

Breed smarter. Make the best possible use of the genetic diversity in the gene pool. Avoid multiple breedings, use dogs from underrepresented lines, and breed 2 or 3 pups from a litter instead of just one. 
Use information about genetic relatedness (i.e., kinship coefficients) to select less related dogs to breed to. This will reduce inbreeding and the risk of genetic disorders.

NO Popular Sires. ​

Add fresh genes to the gene pool using dogs from the country of origin. Type can be restored in a generation or two. Health cannot be improved without replacing genes that have been lost. You can’t have type without health.

Instead of just worrying about your next litter, practice breed-wide genetic management.

Keep an up to date pedigree database so you know what animals you have and who they are related to.

Analyze the pedigree data on a regular basis to monitor the genetic status of the breed.
Work with population geneticists to design an efficient strategy for introducing new dogs to the population. Follow the plan so every dog counts. ​

Use population genetic management instead of mutation tests to reduce genetic disorders.

You are the custodians of a rare breed derived from land race dogs.​

With sound genetic management and careful breeding by knowledgable breeders, you can continue to produce healthy, beautiful dogs for many generations.

You can't be a dog breeder without worrying about hip dysplasia. It's the single greatest cause of pain and suffering in dogs despite diligent efforts of breeders to reduce risk through selection.

Why have we made so little progress in 50 years? I think there are a number of issues, but one of the most important is that we don't worry as much as we could about environmental (i.e., non-genetic) factors.

The food restricted group not only suffered less pain and loss of mobility, they also lived longer. Only about half of the control group lived longer than 11 years and only 30% survived to 12 years. But about 75% of the dogs in the treatment group survived to 11 years and 50% lived to 13. 

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If you haven't already, please read my recent post, "Assessing genetic diversity and relatedness in dogs using DNA", about methods of assessing relatedness and genetic diversity in dogs. In it I present a brief summary of the comments from a paper just published by Nicholas et al. (2018). I also provide some information from a paper published in 2006 by Oliehoek et al. that evaluated several different ways of estimating relatedness. If you missed that, you should read it now or you won't understand the rest of my comments here.

------->

The method under discussion is used by the genetic diversity test available from UC Davis for dog breeds, breeders should be aware of these potential problems with the accuracy of the test.

You will have noticed that I presented direct quotes from the two papers noted above. I also provided a direct quote from published response by the authors of the first paper. It's important to note that the critical comments were not my opinion, scientific or even personal; they were from two groups of very well known canine population geneticists. I did suggest that the issues might be resolved with data validating the usefulness of the test, and until that is available I would view the test as flawed.

At the end of my blog, I made a big point of the fact that scientists have disagreements all the time, and a lot of the progress made in how we understand the world is the product of critical review and the resulting discussions. The concerns are published and the journal allows the other authors to respond. This is a normal and essential part of the scientific process. These are always civil, respectful debates. If you don't take criticism well, a career as a professional scientists is definitely not for you.

​The current debate on the origin of dogs is a great example of various groups of scientists, each with different ideas, duking it out in the scientific literature, one publication at a time. This note in one of the world's most prestigious journals was published in 2013, and the lively debate still continues. I'm sure that sooner or later, we will figure it out and most scientists will come to a consensus. In the meantime, the critical comments of colleagues focus on details, data, assumptions, and methods. There are no personal attacks. Nobody's credentials are questioned. In fact, the scientists that engage in lively debate all know each other, consider themselves colleagues, and are likely to sit down for coffee when run into each other at meetings.

Science is a community of individuals that are committed to figuring out the truth, even if that means there might be winners and losers in the debate. This is the warp and woof of science, and the debate and process of ferreting out the truth is what I love about it.

I posted links to my blog in various relevant groups, one of which was the ICB Facebook page. Sure enough, the trolls came.
​

This person is associated with BetterBred, a company that is using the Davis test as an online breeding tool. She is known to me, because she has been trolling me for years now, as have a number of people associated with the group at BetterBred. She is not a scientist. She has no comments to make about the substance of my blog post.

I did try to make my post understandable to any breeder, from the lawyer and veterinarian to the dog groomer. But Laura Bernier notes (twice) that she didn't understand it, so her comments are not about the substance of that blog but are persona; her intent is apparently to sully my reputation. I've been a professional scientist for nearly 40 years, I have a long list of publications, a record of more than $1.2M in grant support, and the respect of my peers. Her belittling remarks will have not effect at all on my reputation, and they don't even keep me up at night, but I am concerned that she carries around so much anger. Stress isn't good for your health, and I truly hope she gets the help that she needs.

To be fair, I have to say that nobody has been busier with the personal flogging than the person who runs BetterBred, Natalie Tessier Green. I blocked her long ago, but her posts are sent to me by the people that find them offensive or even appalling. This was posted in one of her private groups for users of the BetterBred website and I was gifted several copies.

Natalie Tessier Green has been trolling me for years. She fosters an environment in her company that normalizes this sort of bad behavior, which is not just unprofessional, but antithetical to the process of science. Comments in Natalie's groups often disparage me; it's very reminiscent of the sort of dialog you would hear between two rival clicks at a junior high school.

I'm especially disappointed that Natalie Tessier Green didn't have a  single thing to say about the concerns expressed about the Davis diversity test, but she does note that "it is wrong on nearly every point". Note that I don't sell any DNA tests. For a time about 2 years ago I took orders from breeders who didn't have enough dogs to qualify for the volume discount, but the price was Embark's and I made no money from it. As the test became more well known, breeders have been able to find enough other people to send in a bulk order so I no longer do this. I do however recommend Embark's test if I'm asked and in my professional opinion that is the test that would best suit the breeder's needs. The ICB Breeder Tool is built around the test results from Embark. But I have no affiliation with them. None. 

I must note here that I am not the only one being trolled. The Dog Diversity Project as well as Embark (which runs their DNA analyses) receive a good volume of hateful Facebook posts from BetterBred. There could be other  organizations that find themselves in the crosshairs of BetterBred.

I'm not bothered at all by the attempts of the folks at BetterBred to affect my reputation, although it does upset people who know me, in both the dog fancy and the scientific community. I am, however, tired of the silly attacks. For each one, I get a flood of copies sent to me from people that spot them and find them offensive enough to bring them to my attention. I have to go delete the post, block the author, and add the comments to my "L&S" folder. Yes, it's gotten tiresome.

So, I have now decided to address this problem another way. I will post noxious comments made by anybody affiliated with BetterBred, including their clients, on my website. I will be liberal with links to the BetterBred site, so the curious can see for themselves the vitriol directed by BetterBred and their fans towards members of the canine scientific community. If the posts continue, I'll even set up a separate section on the ICB website where they can be catalogued and searched so that they show up in Google searches for BetterBred.

If anybody at BetterBred has comments about the two papers I blogged about, they should direct them to the authors of those papers, not me; I was not involved with either of them.

Finally -

"Not enough people call you out, because you just block them because you truly don't have the ability to have a decent debate."

No, Laura Bernier, we are not going to have a "debate" this time either. And you now join the others from BetterBred who are blocked and banned for bad behavior.

Oh dear. I didn't even have time to get a cup of coffee after posting this before comments from BetterBred started appearing in my In box. 

I actually find this one humorous under the circumstances. Considering.

Then a bit later, a dig about mental illness. 
Again, they've been trolling me for years. Yet here I am. Still.
​

Updated 12 July 1:07 pm to include additional comments.

​

13 July 2018 - Spammed by BetterBred

Today I get an email from BetterBred, this one some sort of "announcement", for which they have used a DISPOSABLE, TEMPORARY email address. You know, to avoid spam.


​

 

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​

There are a variety of commercial options available to breeders for assessing the genetic diversity and inbreeding of individual dogs as well as breeds. UC Davis Veterinary Genetics Laboratory offers a test based on microsatellite markers (STRs), and MyDogDNA and Embark Vet offer tests using single nucleotide polymorphisms (SNPs). Microsatellites have been around for decades, while SNP technology has developed rapidly over the last 15 years or so and is increasingly used in genomic studies of animals and plants. Which test is most appropriate for you to use for your own dog will depend on the type of information you need, how you want to use it, and cost effectiveness.

Paper by Oliehoek et al, 2006
​
The effectiveness of methods for estimating relatedness, including the method used by Davis, was examined in a paper by Oliehoek et al (2006). They looked at eight different algorithms, including the one used in the Davis test by Queller & Goodnight (1989), which they refer to as "Q&G". The Q&G estimator was originally designed to estimate relatedness between populations, but with a modification it can be used for pairwise comparisons of individuals.
​

Oliehoek et al. concluded that two of the algorithms they tested, UCS and Q&G (the one used by Davis), performed so poorly as to not merit further consideration. What is meant by "poorest results"? It means that their estimators of relationship deviated significantly from the true relationships, which were known because they used a simulated pedigree database. They felt that the errors were so consequential that they didn't proceed with further testing of these two algorithms.

The problem I suspect Nicholas et al. will have with this is that there is no information provided that directly addresses their concerns about the measurement of genetic variation. Much of the response was about the markers for DLA and was not relevant to the estimation of autosomal genetic variation. Assurances were offered that, in unpublished experiments they did, the addition of 25 microsatellites "did not add anything to the power of the current 33 markers". Further, a comparison of diversity measured with the microsatellite panel and 170K SNPs "found no major differences". However, no data are provided to support either of these statements. It would have been appropriate and useful for them to provide the data and analyses behind these statements, but unfortunately they do not.

The reason the methods and results of research are provided in such detail when published is to support the claims made about the data to the satisfaction of other scientists. Here, we're supposed to just "take their word for it". I think many scientists would be concerned about doing this.

POSTSCRIPT

The layperson might be horrified to read the critical comments about a scientific study from other scientists. Be assured that this is the normal process of science. A scientist can expect every word that comes out of their mouth for their entire career to be scrutinized, assessed, and criticized by their colleagues. The criticism will be direct but never personal. In fact, it could be said that scientists sit around picking away at the work of their colleagues for mental sport. It is interesting, stimulating, even fun, and it often results in useful insights that advance a project or field. It is not "bashing", "slamming", or any of the other many terms I have heard used by dog breeders in these contexts. Indeed, I have never heard these terms used by scientists about each other; they simply are not appropriate because they imply that the comments are unfair, inappropriate, and personal, when they are not. Scientists disagree with each other all the time. It's the normal warp and woof of science.

By way of an example, my own favorite criticism was directed to me by the editor of a journal to which I had sent a manuscript for review very early in my career. Although the reviews were favorable, the editor (whom I knew) told me that he didn't like the statistics I had used and suggested that were he to publish the paper, I would "come to find it an embarrassment" later in my career. I sent the paper to another (better!) journal, which published it. It was well-received, and I have never been embarrassed about it. The editor and I remained friends and colleagues.

REFERENCES
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Nicholas FW, C Mellersh, & T Lewis 2018. Letter to the editor regarding an autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Canine Genetics and Epidemiology 5: 4. DOI 10.1186/s40575-018-0059-7

Oliehoek PA, JJ Windig, JAM van Arendonk, & P Bijma. 2006. Estimating relatedness between individuals in general populations wiht a focus on their use in conservation programs. Genetics 173: 483-496.

Pedersen NC, B Shope, and H Liu. 2017. An autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Canine Genetics and Epidemiology 4:11. DOI 10.1186/s40575-017-0049-1

Pedersen NC, B Shope, and H Liu. 2018. Letter to the editor regarding an autosomal recessive mutation in SCL24A5 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Authors' response. Canine Genetics and Epidemiology 5: 4. DOI 10.1186/s40575-018-0059-7

Genetics has been revolutionized in the last decade by the development of amazing new technology. For decades, geneticists relied on markers called microsatellites, which are stretches of DNA with repeated element that can differ from individual to individual. In closely related animals, the repeated pattern would be similar, whereas the pattern would be more and more dissimilar in animals that are less related. 
​

For many years, SNP technology was very expensive and beyond the reach of the layperson. But the cost has come down dramatically in the last few years, and you can now send off a sample of spit to any of a number of companies that will tell you where your ancestors lived, which of your genes are links to particular traits or diseases, and even the nationalities in your background. What started as "recreational" genomics is now driving advances in diagnosis and treatment of diseases.

SNP technology offers some amazing opportunities to learn about the genes in dogs. Companies are popping up that offer to identify the breeds in a mix (some with better success than others). For breeders, high resolution SNP genotyping is providing data that can be used with powerful analysis tools in molecular biology and population genetics to improve our ability to select for the traits we want and against the ones we don't more efficiently than ever before. In fact, livestock breeders can now take a DNA sample from an animal at birth and know the traits the animal will have as an adult. Could we be using these techniques to breed better dogs?

How we can use SNP genotyping to manage genetic disease
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We can use the power of high resolution SNP analysis to reveal the details of genetic relationships among animals. A potential sire that might look like an outcross to your bitch on paper can instead be very similar genetically because of relationships among ancestors many generations back in the pedigree. When you are  choosing a sire to improve a trait, reduce the risk of genetic disease, or increase the genetic diversity in your line, reliable information about the DNA in the dogs can be the difference between success and failure. Let's look at an example of how we can use information about genetic relationships to manage a genetic disorder in dogs.

An organization breeding Labradors for guide dogs was having a problem with elbow dysplasia (ED) (Ubbink et al 1998). They had good pedigree records and used these to map the genetic relationships among the dogs in their breeding stock using kinship to determine relatedness and a technique called cluster analysis to form clusters of related dogs.

This is a "dendrogram", a diagram similar to the branches of a tree that displays the genetic relationships among animals. On the right side of the chart is a numeric scale of relatedness. The shortest branches indicate the highest similarity between individuals; so the very short branches at the level of 0.125 (red arrow), reflect relatedness comparable to a half-sib mating. The next number, 0.0625, corresponds to the relatedness (inbreeding) produced by mating first cousins, and the numbers above that correspond to successively lower degrees of relatedness.

Using SNP genotyping to map genetic relationships

Many breeds are highly inbred and have low genetic diversity. Will this technique using DNA to establish genetic relatedness work for purebred dogs?

I have gathered some DNA data in public archives from published studies that were analyzed using high density SNP genotyping, then used cluster analysis (as was done above) to produce the map of genetic relatedness for a number of breeds. These are displayed below, and many show that there are genetically distinct subpopulations within a breed that could be exploited to look for patterns in the expression of genetic disorders. We know nothing about who these dogs are, but the charts show that there is sufficient genetic differentiation in a breed to use for this type of analysis. On each one I have indicated with a red square the first major division to make it easier for you to visualize the groups. For some of these we clearly need more data, and for all of them we need data for known dogs. But this should give you a good idea of what some of these look like.

Can we do this for your breed?

Here we describe a very powerful technique to sort out genetic relationships among individuals that can be used to improve genetic management of disorders without knowing the genes involved. There is a long list of inherited disorders that breeders are struggling to manage in the absence of genetic information for guidance. Epilepsy, cancer, heart disorders, kidney disease, neurological problems, degenerative myelopathy, and the list goes on and on. We're not making much progress.

We can do this now. We need DNA genotype data for current dogs, including those in the breeding population, to establish the genetic subgroupings within the breed. We need the incidence data for the disorders of interest.

​It might not take a lot of data to reveal the information we need. In the example of Laboradors above, data from just a few dogs would indicate the location of the cluster containing the affected dogs. You could take action using this information far sooner than if you needed 20 affected and 20 clear dogs to search for genes. 

If you're interested in using this powerful technique for your breed, please contact us. We can set up a Genetic Management Workshop for your breed where breeders and PhD population geneticists with expertise in canine genomics and breeding can discuss goals and resources, and work together to develop a breeding plan to address problems. 

We now have amazing tools to help breeders manage the growing list of genetic disorders in dogs. Let's use them!

Even 100 years ago, breeders of domestic animals realized that continuous inbreeding resulted in deterioration in the quality of their stock. To remedy this, every few generations a relatively unrelated animal would be crossed in to the population to freshen up the gene pool and reduce the level of inbreeding. In fact, the coefficient of inbreeding was devised in the 1920s as a way to estimate the level of inbreeding so breeders would know when it was time to do an outcross.

Many modern dog breeders follow a similar regime, breeding close for a few generations then out to a relatively unrelated dog. But is this as effective as we think it is?

For one thing, our dogs are much more inbred than they were a century ago. Many breeds have average levels of inbreeding above 20%, and too many are even higher. With such high levels of inbreeding and low genetic diversity, the dogs in a breed can all be more similar genetically than half- or even full siblings - or even more. How much can you expect to gain from an "outcross" that really amounts to close inbreeding?

They found that a single outcross followed by one or more generations of backcrossing reduced the beneficial effect of the outcross and sometimes even increased the rate of inbreeding. In the cross breeding, the first generation receives 50% of alleles from each of the donor and recipient parents. But in subsequent backcrosses, half of the donor genes are lost on average, so that after a few backcrosses the remaining donor contribution was inconsequential.

This result is not unexpectded, but it should give pause to those that undertake a crossing program that consists of a single donor cross followed by serial backcrosses. Kennel clubs typically prefer 3 backcrosses before admitting the descendants of a crossbreeding program to the studbook. But the simulations show that the required backcrosses essentially flush the donor genes from the recipient gene pool and there is no net benefit. Indeed, there are multiple examples of crossbreeding programs that failed or produced little benefit because the introduced genetic variation was subsequently lost.

Regular outcrossing was the most effective strategy for reducing the rate of inbreeding in the Saarloos Wolfhond, but still the outcomes of the simulations were highly variable. The scenario of regular outcrossing generally reduced the rate of inbreeding, but the inbreeding rates were highly variable, and in some simulations all of the donor genetic contribution was lost. 

What this study clearly showed is that using outcrossing to reduce the rate of inbreeding requires careful management in order to ensure success, and the benefit achieved will be small unless crossing is done on a regular basis. One key to success is to follow outcrossing with strategies to increase the effective population size.  Otherwise, inbreeding will quickly return to previous levels. 

This outcross simulation used a completely unrelated (fictitious) breed as a donor. For breeders that are crossing to what they hope are relatively unrelated dogs in their own breed, the benefit will be much less if the level of relatedness among individuals is high. 

You can now enroll your breed in the new ICB Genomic Management Workshops, in which breeders and expert scientists will work together to assess the genetic status of your breed and design effective breeding strategies to reduce inbreeding, increase genetic diversity, and improve the health of the dogs.

We are accepting breeds now, so don't miss this opportunity to be one of the first we work with in the flagship program. You can read more about the new ICB Genomic Management Workshops HERE. 

Don't miss out on our "Incentive" offer of a free course for each participant for the first three breeds enrolled!

REFERENCES

Windig JJ & HP Doekes. 2018. Limits to genetic rescue by outcross in pedigree dogs. Journal of Animal Breeding and Genetics 135:238-248.

It's the classic scene. The family sits down at the dinner table and Billy grimaces at the food on his plate. He hates peas. HATES peas. So while acting non-chalant and seeming to really dig into his meal, Billy was actually deftly using his fork to push one pea to the other side of the plate, and another up under the thigh bone from his drumstick. A few disappeared under the pile of mashed potatoes, one leaped from the plate and fell to the floor, and soon it looked like he had done a decent job of getting down most of the despised peas.

But Mom is no fool. "Billy", she says sternly, "eat your peas instead of just pushing them around on the plate!" Busted.

We risk doing a similar thing when making decisions about the ideal sire and dam for the next litter of puppies. Let's say you have a bitch you want to breed and you're considering four or five potential sires. You also have some DNA test information that allows you to compare the genetic similarity of the bitch with each of the sire candidates. Selecting the sire that is least similar to the dam should produce puppies with the lowest average inbreeding.

But does this tell you everything you need to know? Are you really improving genetic diversity? Or are you just pushing the peas around on the plate?

Let's consider 2 things. First, let's look at genetic relatedness.

By "relatedness", we refer to the genetic similarity of a dog to the other dogs in the population. Closely related dogs will be more similar; distant relatives will be less similar. 

There will always be genetic differences between two dogs, no matter how closely related they are, because no two puppies will inherit exactly the same alleles out of all the zillions of possible combinations. So even among closely related dogs, you should always be able to identify a dog that is "least" related, and if you're shopping for sires this one might look like the best bet. 

The problem here is that you can identify a dog that is less related compared to the others, but it might still be very closely related - much more closely related than you would risk breeding to if you knew the actual genetic level of relatedness (First cousins? Half-siblings? Full siblings???).

Let's consider an example. We have a population of about 80 dogs in a particular breed, and you are sorting through them to identify which of the sires you are considering is least similar to your bitch. You make your choice and since they don't share any common ancestors for several generations, you're happy.

But the kinship coefficients of the dogs would tell a different story. The kinship coefficient for a pair of dogs is the fraction of their genes that are identical by descent. This sounds like it's related to inbreeding, and it is. In fact, the inbreeding coefficient of a dog (the fraction of the genes in an individual that are identical by descent) is equal to the kinship coefficient of its parents. Since we know that most genetic disorders in dogs are caused by recessive mutations, the kinship coefficient also tells us the risk of producing a genetic disorder caused by a recessive mutation in the puppies.

If you determine the kinship coefficients between the bitch and each of the potential sires, you choose the one with  the lowest kinship coefficient. However, the kinship coefficient reveals that this "least related" dog is actually more similar to the bitch genetically than you would expect of a full sibling. The data for the kinship coefficients with these potential sires are:

Sire number 5 has the lowest kinship coefficient so is least related. But that kinship coefficient indicates that he and the bitch are more similar genetically than you would expect for full siblings, which would have a kinship coefficient of 0.25.

Wow. You wouldn't do a full sibling mating, and this mating would be a similarly close inbreeding. From the data for the other sires, it looks like there is very high relatedness among many of the dogs in the population, whose kinship coefficients go as high as 0.693!

When you compared the dogs relative to each other, one dog looked like a good choice. But after looking at the actual kinship coefficients of the potential parents, you decide that the marriage is much too close for comfort.

Above, I noted that there were two things we needed to consider when making mate selections based on information about relatedness from DNA data. The first was the absolute, and not just the relative, genetic relatedness.

The second issue comes from the first. Genetically similar dogs will have similar mutations. The least related pair based on kinship coefficients will nevertheless share many mutations if they are as similar as full siblings. They might be from different lines and not share any kin for many generations, but genetic similarity brings with it high risk of producing a genetic disorder. Mating of full siblings, with a kinship coefficient of 0.25, has a 25% risk of pairing up two recessive mutations.

Let's look at another example using this same breed. Below is a "dendrogram", a family tree that is based on kinship coefficients determined using a high-density (> 200,000 markers) SNP panel that has considerable power for resolving relatedness among closely related individuals.

On the panel on the left, I have indicated the results of genetic testing for the mutation (VWF) responsible for von Willebrand's disease in this particular breed. Individuals that tested clear have a little "c" at the left end of the branch. Individuals that are carriers of the mutation have two asterisks (**), and dogs that are homozygous (and therefore affected by the disorder) are indicated with four asterisks (****).

You should be able to scan from the top of the chart to the bottom and easily pick out the clear, carrier, and affected dogs. What you will probably notice is that the VWF mutation is widespread in this breed. If there wasn't a test for this disorder, you might think you're avoiding it by choosing dogs that are not closely related to each other. But, as we saw above, all of these dogs are very similar genetically, regardless of how unrelated they might appear on paper.

By Carol Beuchat PhD

ICB is proud to announce a new program for breeders, the ICB Genetic Management Workshops. Now for the first time, breeders can get a scientific assessment of the genetic status of their breed as well as professional guidance in setting up a breeding program aimed at improving the health of their dogs. 

The Workshops will partner breeders with veterinary and population geneticists to do a detailed assessment of the genetic health their breed using both DNA and pedigree information. Then the scientists will work with the breeders to design a breeding program that will address the genetic issues and provide a foundation for sustainably breeding healthy dogs into the future.

The mission of ICB since it was founded in 2012 is to provide purebred dog breeders with the tools and information they need to make breeding decisions that will improve the health of dogs. Breeders will have unparalleled access to guidance from world experts in canine genetics, as well as the tools and expertise of conservation geneticists.

About the Workshops
The ICB Genetic Management Workshops will be ICB's flagship program and the first of its kind. In these Workshops, breeders and scientists will sit down together, evaluate the genetic status of the breed, diagnose the problems, and come up with breeding strategies and recommendations that will improve health. The goal will be to provide a plan that is feasible for breeders to follow and which will have short- and long-term outcomes for health improvement. Genetic assessment of a breed and development of breeding strategies will use the the new ICB Breeder Tool. It will provide breeders with a detailed assessment of the genetic health and issues of their breed and the information they need for making the best possible breeding decisions going forward.

Genetic Assessment from DNA
The genetic assessment of the breed will use DNA genotyping and mutation testing information. The current commercial provider of suitable data is Embark Vet, which uses a state-of-the-art, high-density Illumina SNP analysis with more than 200,000 markers distributed over the entire genome, including all 38 autosomes, the sex chromosomes, and mitochondrial DNA. This is the same platform used by canine genetics research laboratories worldwide and provides the most comprehensive and detailed analysis available. Because this platform is so widely used, marker data produced by research laboratories can be added to our databases to increase our sample size and the breadth of the gene pool represented. 

Genetic and Demographic Assessment From Pedigree Data
Assessment of the genetic status of the breed should ideally include a pedigree database, which provides information about the genetic history of the breed, founder dogs, bottlenecks, changes in population size.  Information from the DNA analyses can be used to verify pedigree relationships. In the absence of a useable pedigree database (e.g., because of errors, missing data), the DNA can be used to establish the genetic relationships of the current dogs, which will provide the information needed by breeders for genetic management going forward.

A good pedigree database, or genealogy reconstructed from DNA data, can be used to locate the genes causing a genetic issue without needing to identify the specific genes responsible. This is especially valuable for complex and polygenic disorders for which it would be difficult and expensive to identify the causative alleles (e.g., cancer, epilepsy). A pedigree database also provides the foundation for estimated breeding values (EBVs), which substantially improve the efficiency of selection.

Our Goals
The Breed Workshops are not courses, although the participants will surely learn a lot. Our overriding goal is to solve problems and provide breeders with the guidance necessary to work towards healthier dogs when planning their very next litter. 

Commitment
The Breeder Workshops involve a partnership with a shared commitment from both the ICB team that is working with the breeders, as well as from the breeders, who need to be willing to commit to implementing the plan produced by the workshop. If breeders cannot make a commitment to implement the strategies they have developed with the assistance of the scientific team, we will not accept them for a workshop. We want to see RESULTS that make a significant difference in the health and welfare of dogs.

For this reason, we have some basic requirements before we will agree to run a workshop for a breed. Any plan will require  the breeding of dogs, so we must have sufficient breeders involved to support this. We will also need to know that the puppies produced can be placed in homes that will properly care for them and retain them until they can be bred if they are suitable. This will probably require many non-breeder participants. People that have left breeds because of  their  health issues might be ideal for raising puppies produced in the program.

The minimum involvement for a workshop is 50 participants with a fee of $200 ea. These can be breeders as well as non-breeders who wish to support the effort. For large breeds, it will take a substantial commitment by breeders to make a meaningful improvement in the genetics of the breed. A few enthusiastic breeders cannot make a significant difference. This will need to be a substantial, collaborative effort with a long-term commitment. With proper planning and scientific support, the breeding program has the greatest chance of success.

Arranging a Breed Workshop
Any group of breeders can request a workshop for their breed. It would be ideal to have club support, but if that is not forthcoming we will work with a group of independent breeders that can meet the requirements for participation and commitment.

We will need the DNA genotyping results from Embark (or other sources using the Illumina canine SNP chip) for a sufficient number of dogs to be able to do meaningful analyses. For some breeds, there are data already available for anonymous dogs from research studies to provide baseline information about the breed. Participants will add to this the genotyping and mutation/trait testing information for current dogs as necessary to fill any gaps and to provide the information needed about the current breeding population of dogs. There is a table below with a current inventory of data, to which data will be added on an ongoing basis from research studies as well as dogs in the breeding population.
​

How Long Will It Last?
If we have the necessary information organized properly ahead of time, we anticipate that analysis and design of a breeding program should take 8 to 10 weeks. But we'll keep working until we're done. The final product is a breeding strategy to be implemented by workshop participants.
​

What You Will Need
This will be work, for both the participants and the scientists involved. It will be a commitment of time as well as learning so that participants understand the rationale for the breeding plan and its goals. You will need enthusiasm and dedication to the project for the long term if you are truly going to make a difference.

We will need the genetic data files from analysis using the Illumina SNP chip, either from Embark or research projects using the Illumina chip. DNA analyses from the Davis genetic diversity program use microsatellites (STRs); the data are not compatible with data from other sources and lack the resolution of the SNP data. Mutation testing from MyDogDNA/Mars can be used, but their DNA genotyping data is not compatible because they use a proprietary chip. So, stick with Embark if you do any commercial DNA analyses.

We will be accepting breeds for workshops on a first-come, first-served basis. We need a commitment with payment for at least the minimum 50 participants at $200 ea to get a reserved spot on the calendar. If small breeds are unable to meet the requirement of 50 participants, please contact us to discuss whether we can design a program for the breed with fewer breeders.
​

Data Already Available
DNA data already available for some breeds that can be used in analyses. We have data for most AKC breeds and at least 50 dogs of these breeds (# in parentheses):

• American Cocker Spaniel (70)
• Border Collie (50)
• Boxer (160)
• Cairn Terrier (60)
• Cavalier King Charles Spaniel (50)
• English Setter (80)
• English Springer Spaniel (50)
• German Shepherd (130)
• Golden Retriever (250)
• Irish Wolfhound (210)
• Labrador Retriever (630)
• Maltese (80)
• Miniature Schnauzer (60)
• Rottweiler (80)
• Vizsla (90)
• Yorkshire Terrier (180)​

Enroll for a Genetic Management Workshop
We are scheduling workshops on a first-come, first-served basis. You will need a minimum commitment of 50 participants. 

Please contact us to discuss setting up a Genetic Management Workshop for your breed.

​
Contact:

Carol Beuchat PhD
Scientific Director
Institute of Canine Biology
carol@instituteofcaninebiology.org

To learn more about the genetics of dogs, check out
ICB's online courses

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​

Sewell Wright, who first formulated the method for estimating inbreeding from pedigrees (hence, "Wright's Coefficient of Inbreeding"), also described another way of assessing inbreeding using something called a "fixation index", or Fis.

In a large, genetically diverse population in which mating is random, you would expect inbreeding to occur only rarely because the probability of two related individuals mating is low. If we were to find that there was a higher level of inbreeding in this population than what would be expected just by chance, that would be evidence of non-random mating of related individuals; i.e., preferential inbreeding.

If we know the allele frequencies of a particular marker in the population, we can estimate the genotypes to expect under random mating. These would be predicted by the "Hardy-Weinberg Equation" (p^2 + 2pq + q^2), where p and q are the frequencies of the two alleles for the marker of interest. We can use the Hardy-Weinberg equation to predict genotype frequencies under random mating in a population. If we measure the actual genotype frequencies and find them to be different than expected based on H-W, then we know that mating has not been random.

We can use this tool to detect non-random mating using Wright's fixation index, Fis. Animals in a population with a level of inbreeding higher than expected based on H-W will have a positive Fis statistic. Animals that are outbred relative to what is expected under H-W will have a negative F statistic. An Fis of zero indicates a level of inbreeding equal to the expected value based on allele frequencies in the populaion.

In a nutshell, a positive Fis indicates inbreeding; a negative Fis indicates avoidance of inbreeding.

We can use our thousands of SNP markers to estimate Wright's Fis statistic for a population of individuals in a breed. The graphs below show the distribution of inbreeding coefficients (Fis) in Boxers and Irish Wolfhounds. For both breeds, there is "excess homozygosity" - a higher incidence of homozygosity on average than you would expect to see in a randomly breeding population. In both breeds, breeders are preferentially mating dogs that are more related than average in the population to produce higher levels of inbreeding.

 
These data show that better choices when selecting breeding pairs could slow the rate of increase in inbreeding in both breeds and also lower the risk of genetic disorders caused by recessive mutations. 

The Coefficient of Inbreeding (COI)
Most breeders are familiar with Wright's Coefficient of Inbreeding (COI), which can be calculated from pedigree data. The COI provides an estimate of the predicted level of inbreeding based on the simple assumptions that alleles are inherited independently and with equal probability. From this, you can predict the average COI of the litter of puppies produced by a pair of dogs. Because COI is based on the probability of inheriting alleles across all generations of a pedigree, it cannot predict the COI of a dog exactly; only the average and the expected variation. However, it usually correlates well enough with "realized" inbreeding (based on DNA homozygosity) that it remains the single most useful statistic used by animal and plant breeders today to assess the level of inbreeding in an individual or the inbreeding to be expected from a particular breeding.

Runs of Homozygosity (ROH)
The most common method of determining inbreeding from DNA data uses a technique that quantifies the amount of inbreeding represented in "runs of homozygosity" (ROH), which are regions of the chromosomes where there are many consecutive homozygoous loci (Ceballos et al. 2018; Curik et al 2014).

The homozygosity produced by inbreeding is not randomly scattered all over the chromosomes. Selection, both natural and artificial, will produce "hot spots" of homozygosity in the regions of the chromosome where there are genes under selection (Sams & Boyko 2018). If the genes remain under continuous selection over generations, as would be the case for the genes for type in a purebred dog population, the blocks of homozygosity will tend to get longer and longer each generation (Kim et al. 2015). 

​Let's look at some examples.

There are panels below for two breeds. The horizontal strip at the top represents the chromosomes lined up end to end to form a continuous strip the width of this page, with each of the autosomal chromosomes numbered consequitively from 1 to 38.

I've blown up a part of the strip to show you the first 7 of 38 chromosomes.
​​
Below this is a chart depicting the blocks of homozygosity for about 80 Coton de Tulear, with each dog represented by a horizontal strip with dog IDs indicated on the left. Below this is a similar chart for a similar population of Stabyhouns. SNPs that are heterozygous are pink, while homozygous SNPs are blue.

​You can see scattered across the chromosomes for the individual dogs that there are blocks of blue of various sizes. These are the runs of homozygosity. 

Shared Homozygosity
Something you will notice is that there are regions that are homozygous in multiple dogs, which is evident because they appear as vertical blue line across the rows where these regions all line up. There is an obvious one in chromosome 23 in the Stabyhoun, which shows up as a blue stripe about 25% from the right edge of the chart. There are other areas of shared homozygosity here and there in both breeds.
​

Besides usefulness as a measure of inbreeding, runs of homozygosity are also relevant because they are enriched for deleterious mutations. That is, mutations get trapped in blocks of inbreeding and cause the genetic load of detrimental mutations to increase over the generations. If breeders can see where blocks of homozygosity are in the genome, they can select sires that do not share the same ROH, which will prevent the blocks from being passed on to offspring. The two individuals might have the same amount of inbreeding but distributed differently across the genome, and being able to visualize the actual inbreeding on the chromosomes can allow breeders to break up blocks using the heterozygosity at the same place in other parent.

Although there seems to be general agreement that ROH currently the method of choice for estimating the level of inbreeding from DNA, there is still discussion about the size of the blocks of homozygosity to include in the calculation (Sams & Boyko 2018). Certainly, the longest blocks represent the most recent inbreeding and should be considered, but should older inbreeding also be included? This can amount to a substantial difference in inbreeding estimates, and as yet there is no consensus on what provides the best estimate. In the meantime, comparisons should be made among individuals or between breeds using the same minimum block size, which should provide comparable estimates of the most recent inbreeding.

You can learn more about runs of homozygosity and how to use ROH to estimate inbreeding in the two-part tutorial below.

ROH Tutorial: part 1
​ROH Tutorial: part 2

REFERENCES

Curik I, M Ferencakovic, & J Solkner. 2014. Inbreeding and runs of homozygosity: a possible solution. Livestock Science 166: 26-34.

Ceballos FC, PK Joshi, DW Clark, M Ramsay, & JF Wilson. 2018. Runs of homozygosity: windows into population history and trait architecture. Nature Reviews Genetics 19: 220-234. 

Kim E-S, TS Sonstegard, CP Van Tassell, G Wiggans, & MF Rothschild. 2015. The relationship between runs of homozygosity and inbreeding in Jersey Cattle under selection. PLoS ONE 10:e0129967. https://doi.org/10.1371/journal.pone.0129967.

Marsden CD, D )rtega-Del Vecchyo, DP O'Brien, and others. 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. PNAS 113: 152-157.

Sams AJ & AR Boyko. MS. Fine-scale resolution and analysis of runs of homozygosity in domestic dogs. bioRxiv preprint (7 May 2018). doi: http://dx.doi.org/10.1101/315770.

By Carol Beuchat PhD

One of the most basic things to know both about a breed and an individual dog is genetic diversity. In a breed, genetic diversity is the variation in DNA that results in the differences in traits from individual to individual. Genetic diversity also allows populations to adapt or evolve in the face of changes in the environment or disease. 

In an individual animal, genetic diversity is realized in the fraction of loci that are heterozygous. Inbreeding increases the fraction of loci that are homozygous, and this in turn raises the risk of the expression of a recessive genetic disorder. Homozygosity also results in an overall deterioration in health referred to as "inbreeding depression". So, at both the individual and population (i.e., breed) levels, it is important for breeders to be monitoring genetic diversity.

There are several different ways to assess genetic diversity using SNP data. Below I will describe how each is estimated, what the data mean, and how breeders can use the information.
​

A very common method of assessing genetic diversity from DNA data is by computing heterozygosity.

A locus with two copies of the same nucleotide (e.g., AA, aa) is homozygous. A locus with two different nucleotides (Aa) is heterozygous. This is part of the data spreadsheet from SNP genotype which lists the genotypes found at 4 SNP markers (e.g., BICF2G...., etc) on the chromosomes of 12 dogs (one in each row). 

For the first marker (column 618), you can see that some dogs are homozygous for that SNP (either AA or GG), while some are heterozygous (AG). For the next two SNPs, all but one of the dogs are homozygous for the same nucleotides, and all of the dogs are homozygous at the last marker.

​We can determine the degree of heterozygosity of each of these markers by tallying up the different combinations of alleles for each marker in each of the dogs in our sample. From these information, we can then compute heterozygosity, which is simply the fraction of all of the marker that were heterozygous, averaged over all of the dogs. The higher the heterozygosity, the greater the genetic diversity. This is usually referred to as "observed heterozygosity" (Ho).

The graphs below show the frequency distribution of observed heterozygosity (Ho) determined for dogs in four different breeds: the Labrador and Golden Retrievers, the Coton de Tulear, and the Stabyhoun. You can see immediately that although there are dogs in both of the retrievers with low heterozygosity (0.2 or lower), there is some variation in the population such that the distribution extends up to about 0.35.  The average and minimum Ho are similar to these in the Coton de Tulear, but the highest heterozygosity is about 0.3. The population of Stabyhoun has the lowest heterozygosity with most individuals less than about 0.25 and little variation around the mean of 0.2.

The data for heterozygosity for these four breeds reveal that the Labrador and Golden have the highest average heterozygosity, the Coton de Tulear, somewhat less, and the Stabyhoun the least. Individual dogs with the highest values for Ho will produce puppies with lower levels of inbreeding on average than dogs with lower Ho.
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The world of the dog breeder is undergoing a sea change. We have had DNA tests for individual mutations for   a few years, but now (finally!) breeders can get a genotype that documents the DNA of all 38 autosomal chromosomes, the two sex chromosomes, and even the mitochondrial DNA. This is a massive amount of data - the file for a single dog has one row and more than 200,000 columns. 

These DNA tests are using what is now the gold standard for plant and animal genotyping. This technology uses markers called single nucleotide polymorphisms (SNPs), which are just what the name says - a locus on the chromosome at which the nucleotide present can be an A, C, T, or G. These nucleotides are the "alphabet" of DNA, a code that contains the instructions for making a protein that has some function in the body. The SNPs used as markers tend to be variable, or polymorphic, and this variation allows us to use them to estimate genetic diversity, determine the relatedness of animals, and even visualize the distribution of homozygosity (inbreeding) on the chromosomes. The massive amount of information contained in a SNP genotype, together with the reduction in cost over the last few years, have made this technology the method of choice for most genetic studies in both plants and animals. 

SNP genotyping of dogs is now commercially available at a reasonable price ($100-200), and breeders are jumping at the chance to take advantage of this new tool. But in many cases the breeder with raw data file in hand doesn't know what to do with it. The thousands of columns of nucleotide data reveal no information that a breeder can translate. So how can we make it useful?

With the right software and some expertise in population genetics, we can extract a tremendous amount of information from the file for an individual dogs, and even more if we have data for a modest sample of dogs in the breed. The technology is too new for books or online resources designed for use by the layperson or dog breeder. But I am summarizing in a series of posts the basic information breeders need to understand what their data mean and how they can use it.

First, I will review the basic tools that can be used by breeders to assess the genetic status of their breed. These evaluate genetic diversity, genetic relationships, and population structure. Then I will show how to use the data for individual dogs when evaluating the suitability of potential mating pairs. Finally, I will provide examples of some resources that breeders can use to develop breeding strategies for sound genetic management and to reduce the incidence of genetic disorders in a breed, including the use of cross-breeding programs when necessary to restore genetic health.
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​A DNA Primer for Dog Breeders

Quick Start Guide

1) Genetic Diversity

• Heterozygosity (Ho)
• Inbreeding (Runs of Homozygosity)
• Inbreeding (Fis)

2) Relationships

• Kinship Coefficient
• Mean Kinship (genetic value)
• Kinship Matrix
• Dendrograms

3) Population Structure

• Principal Components Analysis

​

The most basic tool of the dog breeder is the pedigree. In essence, it is the documentation of the genetic and demographic  history of an animal, and it can hold a treasure trove of useful information.

Often, however, the quality of the pedigree information available for a dog is not what you would like it to be. Most often, dog pedigrees are incomplete, either not including generations back to the founding of the breed, or missing animals in the subsequent generations. Of course, there are also errors, both deliberate and inadvertent, that can change the historical picture. Finally, a pedigree database might exist for a breed but is not accessible, perhaps for technical reasons such as a computer platform that does not communicate well with the rest of the world (e.g., self-designed pedigree software), an out-of-date computer (yes, there are still data being kept on old Commodore computers...), or not computerized at all (think folders of paper). Perhaps the most distressing reason for lack of accessibility is the unwillingness of people who have custody of the information to allow public access. (This means you too, AKC.) It's hard for me to imagine how anyone could argue that this is in the best interests of the breed; it can only be selfish or ego-driven in someone who fails to see that data that can't be used might just as well not exist. These databases die with their creators, with the records being tossed out by relatives or even strangers who see no value in them. Such as waste.

For breeds without an adequate pedigree database for whatever reason, the data produced by SNP testing can be used to reconstruct the genetic relationships among all of the individuals you can get samples for. Software compares the similarity of the genotypes based on SNPs among the tested individuals. From this information, a tree can be constructed that displays the organization and degree of relatedness among the members of the population. This is based on the same information as used to create a kinship matrix.

In the chart below, I have used the SNP genotyping information for a group of dogs to reconstruct their pedigree relationships based on genetic similarity. The tree structure outside the square is the "family tree" illustrated as a dendrogram. (Learn how to read a dendrogram HERE.) The square in the middle is a "heat map" of the kinship values that depicts at just a glance the degree of relatedness of groups of animals in the breed as reflected in the dendrogram. (Learn how to read heat maps HERE.) The same animals are on both axes in this heat map, so it is symmetrical across the diagonal. (You can match up the clusters across the top with those along the left axis.)

In the absence of pedigree information, I have been able to reconstruct the genetic relationships among this group of dogs using a very large number of SNP markers that are distributed across all of the chromosomes. Where pedigree information is not available or is incomplete, this tree of relationships can be used to establish the genetics of an existing population of animals. If good pedigree records are kept going forward, they can be an excellent tool for assessing relationships among individuals and making predictions of litter inbreeding coefficients without the cost and logistic hassles of DNA analysis. The pedigree relationships can also inform the strategic choice of animals to be genotyped in the situations where that information is needed (e.g., trait or mutation testing).

​For breeders trying to breed more strategically to reduce the incidence of genetic disorders in their dogs, but might not have the best pedigree information, DNA analysis using high density SNP markers can provide research quality genetic information for a modest cost. We can convert the data for thousands of SNPs into a chart that displays the true genetic relationships among a group of dogs. 

By Carol Beuchat PhD

It is often assumed that dogs are carnivores like the wolf. However, one of the significant changes that occurred with domestication was in the genes involved in digestion. One of these that is especially significant is in the gene coding for pancreatic amylase (AMY2B), which breaks down starch into the sugar maltose in the small intestine. Related carnivores like the wolf, coyote, and golden jackal have two copies of the AMY2B gene. Most dogs, however, have more than this, and in some cases many-fold more. These duplicate copies of a gene are called "copy number variations", and they can occur during DNA replication. In the case of the amylase gene, dogs with more copies of the gene produce more of the enzyme amylase, which allows them to digest starch more efficiently.
In this chart, the dogs with two or very few copies of the gene include the most primitive breeds and some of the spitzes (Dingo, Greenland Dog, Siberian Husky, Pug, Laika, etc). Among breeds that typically average more than 12 copies of the gene are the English Springer Spaniel, German Shepherd, Rottweiler, Border Collie, and whippet. The breed with the most AMY2B copies determined so far is the Tazi, with an average of about 18 and some individuals with more than 20.
​

How would dogs benefit from extra copies of a gene for starch digestion? Dogs followed humans around the globe and lived where they did, and what was available to eat locally would be reflected in the diet of both. One of the key innovations that allowed expansion of humans across Asia and into Europe was agriculture - the ability to keep livestock and to grow crops for food.

Dogs were used to guard and manage livestock, but the animals were how shepherds made their living and were extremely valuable. They were not the food source for the shepherd and his dogs. Instead, they were used as a renewable resource, providing milk on a regular basis and reproducing yearly to produce the income of the next season. Eating the livestock would be self-defeating, like spending the principal in a savings account instead of just living on the funds produced by earned interest. Instead, the dogs and their shepherds lived primarily on their renewable resources, grain and milk, perhaps with an occasional wild animal for meat, so both had diets that were high in starch. Dogs with more copies of the AMY2B gene would be more efficient at digesting starch, and if this was a major component of the diet it would drive selection for an increase in the number of copies of the gene.

What is the evidence to support this scenario? A survey of dogs from around the world found that dogs from "agrarian" areas (red) had more copies of the AMY2B gene than dogs from "non-agrarian" areas where plant crops were difficult or seasonally impossible to grow and comprised less of the diet of both humans and dogs (blue). You can see from the map below, on which the dash lines mark the approximate extension of prehistoric agriculture, that from the ancestral number of copies of the gene (two) in wolves and other related carnivores, the number of copies increased as much as 11 fold (to 22 in both the Tazi and the New Guinea Singing dog) in dogs from agrarian regions. This held not just for the "breed" dogs, but also for the native village dogs in those areas. The dogs with the fewest copies of the AMY2B gene were from areas where the climate was not suitable for large-scale agriculture, and fish and meat likely formed a greater proportion of the diet (e.g., Greenland dog, Siberian Husky).

So one of the ways in which dogs were changed by their association with humans in most of the world was in their diet. Hunting is time consuming, energy intensive, and dangerous, and the ability to grow crops as a reliable source of food is one of the key events that facilitated the development of human civilization. The common vision of dogs as strict carnivores that get tossed a nice meaty bone for dinner each night is not reflected in what we know about their history and biology. Dogs have adapted physiologically to a diet high in starch, and in much of the world today the diet of working dogs still consists of boiled grain and milk products like whey or cheese.

So, what about all the hype about raw meat diets and grain-free kibble? They are fads, based on ideas instead of science. Clearly, dogs have adaptations for digestion of starch, just like we do, and they also love meat - again, just like we do. But grains have been a major component of the dog's diet for thousands of years and the notion that the "natural" diet of the dog is a big, meaty bone is a myth. If anybody tries to convince you otherwise, demand to see some scientific evidence. You have the scientific sources available here that convincingly demonstrate otherwise.

REFERENCES

Arendt M, KM Cairns, JWO Ballard, P Savolainen, & E Axelsson. Diet adaptation in dog reflects spread of prehistoric agriculture. Heredity 2016: 1-6.

Marciniak S & GH Perry. 2017. Harnessing ancient genomes to study the history of human adaptation. Nature Reviews Genetics 18: 659-674. doi:10.1038/nrg.2017.65 
​
Pennisi E. 2016. How farming changed the dog. Science 360(6391): doi:10.1126/science.aal0353

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Still, even after solving this problem, the test was not doing a very good job of predicting dogs at risk for the disorder. Some dogs that were homozygous for the SOD1 mutation did not develop the disease, and age of onset could vary considerably among breeds. Suspicion grew that other genes might be involved, so further GWAS studies were launched. Researchers identified a "modifier locus" (SP110 nuclear body protein) on chromosome 25 that was present in 40% of affected dogs but only 4% of those unaffected (Ivansson et al. 2016). A particular haplotype of SP110 was associated with increased risk of developing DM as well as earlier onset and was found in 38 breeds with an overall frequency of 38%. SP110 is involved in regulation of gene transcription and may play a role in immune response and many other processes such as response to DNA damage or infection.
​
If all that wasn't bad enough, a study of nearly 34,000 dogs has found the original SOD1 to be widespread among dogs (124 of 222 breeds examined), and at a very high frequency in some dog breeds. (For most of the breeds in which the mutation was not found, sample size was low and the data cannot be used to rule out the possibility of occurrence in those breeds.) This graph for breeds with more than 50 dogs tested was created using the data in the table below from Zeng et al. (2014). If allele frequency (y-axis) = 0.05, half of all individuals had the mutation (A allele); if frequency = 1, all animals had the allele.
​

You can download the table containing all of the data, not just > 50 individuals, here (from Zeng et al. 2014):
Supplementary Table 2 (complete breed incidence data)

With multiple known forms of the SOD1 mutation, widespread distribution of the mutations among many dog breeds, and evidence of a complex interaction with at least one modifier gene, it is clear that the genetics of DM are complex. This is not a disorder that breeders will be able to control with a simple mutation test, and it is very misleading to think of DM as "caused by a mutation". The best strategies for breeders to use for genetic management of DM have not been identified and nobody seems to be addressing this issue, so breeders are making their own decisions and crossing fingers.

The situation is made even more complex because the function of SOD1 is not limited to effects on the nerves for voluntary muscles. In fact, the superoxide dismutase gene produces an enzyme that is a key part of your body's own anti-oxidant defense mechanism. Superoxide dismutase is a "free radical scavenger". Free radicals are highly reactive (oxidative) molecules that are produced by normal metabolic processes but can damage DNA, cells, proteins, and lipids, causing disease. The damaging effects of free radicals are mitigated by the body's antioxidant systems, including superoxide dismutase, and maintaining a balance between the production of free radicals and their inactivation by antioxidants is critical. A mutation in SOD1 doesn't "cause" DM in dogs; it wreaks havoc with the body's essential defense mechanism against  free radicals anywhere in the body, including the nerves to the voluntary muscles.

While many breeders hope for DNA tests that will accurately predict risk of DM in dogs, the reality is that not only is this unlikely to happen, but DM is probably not the only problem this mutation is causing in dogs. There is surely a longer list of negative consequences from the SOD1 mutation in dogs that we have yet to connect with this gene. I predict that this will only become more complicated.

___________________________________________________________________________________

REFERENCES

Awano, T., G.S. Johnson, C.M. Wade, et al. 2009. Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis. PNAS 106: 2794-2799.

Ivansson, E.L., K. Megquier, S.V. Kozyrev, et al. 2016. Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy. PNAS 113: E3091-E3100.
​
Zeng, R. J.R. Coates, G.C. Johnson, and others. 2014. Breed distribution of SOD1 alleles previously associated with canine degenerative myelopathy. J. Veterinary Internal Med. 28: 515-521.

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After I published my blog post yesterday, I was alerted to an article that articulates much of what I had to say. I have appended a note to the bottom of my post, but I copy it here as well so nobody misses it.

There's something that's been bugging me more and more, and today all the little bits I need to grouse about it happened to fall into my lap at the same time. So grouse I will.

We're going to talk about the Newfoundland.

Have a look at some photos and illustrations of the Newfoundland. As you know, it's a relatively old breed, dating back to the creation of the Labrador Retriever from the St. John's Water Dog. The Newfoundland has large size as well as a substantial coat that allow it to work in frigid temperatures on both land and in water. It's a breed that most people recognize on sight, the image of strength, athleticism, nobility, and sweet temperament.

​

There are still Newfoundlands around that look like these dogs. But the selection pressure on this breed - the "trajectory" of selection by breeders - has been for an ever shorter muzzle and a domed skull, creating an outline that no longer looks anything like the original working dog.

The drawing below illustrates the head of the "modern" Newfoundland from show lines. Many are not this extreme, and some are more, and dogs with heads like this are taking home ribbons in good competition.

What you see here is a breed in the process of becoming brachycephalic.

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Interestingly, the heads depicted in AKC breed standard look little like the original rectangular skull of the early dogs. When did the ideal head drift away from the very functional dimensions of a canine athlete to the scaled-up rendition of a toy companion dog? And perhaps the better question is why?
​

As the muzzle becomes shorter, the parts don't become smaller to fit into less space. Instead, the structures that should be in the muzzle get pushed into the front of the skull. Of course, that's where the brain should be, and there really isn't any place for it to go either, so it twists and deforms to accommodate the different space, and it can even get pushed through the hole in the back of the skull where the spinal cord connects to the brain. Note that there really isn't extra room there either, so the vessels that carry blood and spinal fluid to and from the brain and the spinal cord itself get pinched. The result is neurological and anatomical disorders that cause suffering to the dog. Syringomyelia and Chiari-like formation plague several breeds that have become ever more brachicephalic over the generations, especially the Cavalier King Charles Spaniel, Brussels Griffon, Chihuahua, and French Bulldog.  

The other consequence of a shorter muzzle is a reduced ability of the dog to avoid overheating. The "air conditioner" of the dog is in the muzzle. Longer muzzles have a greater ability to cool the dog, which is why we see those long, skinny noses in the Saluki and other breeds that live in hot environments. (Read about the amazing muzzle of the dog.)

​There are other unintended consequences of shortening the muzzle. Pushing the structures of the muzzle into the skull also forces a change in the structure of the palate and airways. The result is difficulty breathing, and surgery to open the airways of the brachycephalic breeds has developed into a brisk business for the veterinary surgeon. The collective effects of the respiratory disorders that result from brachycephaly are referred to now as "Brachycephalic Airway Syndrome". Also under "unintended consequences" is the development of the unsightly "roll over the nose" that results when the bony structures on the inside of the muzzles become shorter without also shortening the skin around it. In toy breeds, the nose roll is considered a "breed feature", even though the rolls can cause skin issues and bacterial infections that require regular treatment.

The serious problems that have been produced in brachycephalic breeds are now the subject of a major effort by kennel clubs and veterinary and welfare organizations in Europe to make those looking for a puppy aware of the serious health issues these dogs face.

So here's the problem. Breeders might like the looks of the shortened muzzle and domed skull on the today's Newfoundland, but should they be allowed to breed for structural features that will compromise the health and function of the dog? 

There is pressure in Europe on breeders to breed away from these extreme features and back towards sound, functional dogs. If we can clearly see that the path ahead for the Newfoundland is towards features that will compromise function, then the time to do something is now. The issue is not "cosmetic"; It is anatomical and physiological, and it consequently affects general welfare as well as pain and suffering.

It's time for a "Head's Up" for breeders. These problems need to be addressed, and fixing them will require involvement of both clubs and judges. The standard could use some changes as well so it's clear that "shorter is better" doesn't apply lest we end up with 150 lb pugs. The necessary changes should not be arbitrary or guessed based on opinions and assumptions of breeders and owners. Scientists with expertise in anatomy and physiology of brachycephalic dogs should be enlisted to work with the breed organizations in outlining the steps that need to be taken to address the problems. There are several labs actively involved in research programs on brachycephalic airway syndrome, and that ready expertise should be stop number one for breed organizations setting out to tackle the muzzle issue.

To be fair, the Newfoundland is not the only breed sliding down the slippery slope to brachycephaly. The other breed that has started catching my eye is the Rottweiler, another heavy-bodied working breed that is not improved by a shorter muzzle. So head's up to the Rottweiler people as well. It's time to make a plan.

As purebred dog breeding faces more intense scrutiny than ever before, it is incumbent upon breeders to ensure that their vision of breed perfection is also compatible with health and function. The trend towards shorter and shorter muzzles in Newfoundlands needs to stop. Breeders and clubs should work with scientists and veterinarians to come up with guidelines for anatomy that will guarantee that muzzle of the Newfoundlands can do what it's designed to do.

UPDATE (27 October 2017)

After I published this post, I was alerted to this great article (written in 2013!) that makes the same points about the changes in the Newfoundland skull. Clearly this isn't a new issue, so what I want to know is what breeders are doing about it. If nothing, then that's a problem, because these are not changes in cosmetics but alterations of structure that have profound effects on function and health.

A short muzzle on a dog like this should be considered a genetic defect by responsible breeders with a commitment to breed for health. If breeders do not see it this way, then there needs to be some oversight by veterinarians and those well-versed in the problems produced by brachycephaly.

What rationale do breeders offer for producing dogs with a head structure that seriously compromises the health and welfare of the animal?

The amazing olfactory abilities of the dog are well-known to any dog owner. With a sniff of the door jamb, my dog knows who is on the other side of the front door before I open it, he can locate one of his toys hidden in a drawer, and he heads straight for the person with treats in their pocket when we go to the dog park. We have made good use of this portable detection system to find lost children, locate bombs, detect cancer, and many, many other things. The dog's nose is truly remarkable.

Just as amazing as its sensitivity to odor is its design, which is much more complex that it might first appear. Inside the muzzle is a complicated system of passages, the turbinates, that both humidify the air and also direct it to the olfactory organ for scent detection. This design must accomplish both respiration and scenting as breathing and sniffing, respectively.

To determine the sensitivity of scent detection, they placed a "smell" source, a chemical called 2,4-dinitrotoluene (DNT), in a small tin with holes in the side to allow vapor to escape. They used sophisticated chemical sensors (ambient ion mass spectroscopy) to document scent detection.

Finally, to visualize the flows of air, they used high speed video and "schlieren imaging", which uses optical techniques to photograph density gradients in air flow, as well as "theater fog" for some demonstrations.

What they found is fascinating. When the dog exhales, air is directed downwards and outwards. When the dog is sniffing a surface, the airflow from exhalation actually draws the odor from the object being scented towards the nose. This effectively extends the "aerodynamic reach" of the nose. The inspiration-expiration cycle during scent detection is repeated very quickly, about 5 times per second.

The air flow patterns that result from the simple design of the dog's nose increase the efficiency of scent detection by 8 times over that for the steady "inspiration" used in scent detection devices. This is achieved simply by directing the exhaled air away from the source of the odor in a way that draws the scent towards the nose. In fact, the farther away the scent, the greater the advantage of the dog's nose over a commercial device with continuous inspiration; in one set of experiments, the dog's nose was 4 times better than the detector at a distance of 10 cm from the source of the scent, and 18 times better at a distance of 20 cm.

Using what they learned from the dog, these researchers were able to construct a "bioinspired" scent detector that "sniffs" instead of continuously drawing in air and directs the exhaled air in a way that draws in scent from the source to the intake. When the air intake was directly above the source of the scent (distance = 0 in the graph below), continuous "inspiration" was as good or better than sniffing. But as the scent source moved away, the advantage of sniffing got better and better.
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Needless, to say, the results of this study should be of great interest to the military and in situations where efficient odor detection is critical. A simple alteration in the design of odor detection devices, inspired by the anatomy of the canine nose, can result in spectacular improvements in efficiency.

Now why didn't we think of that?

REFERENCES

Staymates ME, WA MacCrehan, JL Staymates, and others. 2016. Biomimetic sniffing improves the detection performance of a 3D printed nose of a dog and a commercial trace vapor detector. Scientific Reports 6:36876; DOI: 10.1038/srep36876.