So, what is the source of the problem? Animals in closed populations can only breed to their relatives. All breeding to related dogs is inbreeding. Inbreeding produces homozygosity - two copies of the same allele at a locus. This is a good thing for the genes for type. It's a bad thing for genes that are broken. A genetic disorder is not caused by mutation bombs that you can simply remove to restore health. A genetic disorder is what results when a dog does not inherit a copy of the allele necessary for proper function. So, we have some loci that have two copies of a good allele; but for all the loci that have two copies of a broken allele, something function will be broken.

We are trying to produce healthy dogs by throwing mutations out of the gene pool. But it's a closed, finite gene pool; eventually we will throw all of the genes out. In fact, animals in closed populations go extinct.

Again. Animals in closed populations - aka closed gene pools - go extinct.

There is no "breeder magic" that will prevent this. There is no "science magic" that will prevent this. Animals in closed gene pools go extinct. Some sooner, and some later, but inbreeding will relentlessly increase over time, and diversity will decline, until so much stuff is broken that the animals can no longer reproduce and survive.

All of the other things breeders usually discuss really aren't relevant to addressing this overarching, unavoidable problem. Should we worry about hip scores, or is longevity more important? What about an eye problem that has a late onset? What about mutations with only mild effects? There is lots to talk about, and discussions have continued...for years.

But here's the only problem we need to talk about: inbreeding and loss of genetic diversity.

Fix this problem and you will have healthy dogs. If you start with a population of healthy dogs and randomly remove 40% of the alleles the breed started with, you will most certainly break things. This breed's average inbreeding is more than 40%; if half of that (20%) is homozygosity for good genes, then 20% of it is homozygosity for bad genes. That's a lot of stuff that's broken.

You cannot select your way out of this problem; remember, selection removes alleles, and lost alleles are the problem. It might be possible to restore some lost genetic diversity by strategically using less closely related dogs for breeding. Genetic analyses can reveal if this is possible.

We have much better tools to guide breeding decisions now than simply looking at stacks of pedigrees and comparing health issues. At the very least, you should be using those. You should know the heritability of all of the traits and disorders under selection (0.06? 0.33? 0.89? You should know the size of your gene pool (is it 57, 18, or 6?). You should know the effective population size of the breed (504? 92? 4?). You should know the pairwise kinship of the breeding dogs in the population; the inbreeding data suggest that the dogs are on average as closely related as what you would get from 3 or 4 consecutive full-sib crosses. Would you ever do 3 or 4 full-sib crosses???? In terms of genetics, that's what you have. You need to know which dogs in the breeding population have the highest genetic value so you can be sure to breed those, and which have the lowest value so they can be retired. You should know how much improvement in all of these things is possible if the existing genetic diversity in the breed is used in the most strategic way. If it turns out that this will not be adequate to restore the breed to health, then you need to evaluate strategies that will.

These are things you won't learn about in 20 or 30 years of breeding. You probably don't know anything about effective population size or kinship coefficients or founder genome equivalents. These are not things you will learn by breeding. These come from the science of population genetics that has been developed over the last 100 years by study of thousands and thousands of breeding programs for both domestic and wild animals. These are the tools used by breeders of other domestic animals. They are used in genetically managed programs for service dog breeding; they work for dogs just as they do for any other animal.

To solve the problems in this breed and in purebred dogs, we will have to correctly identify the cause of the problem (inbreeding and loss of genetic diversity), determine the best strategies for addressing the problem, and design a breeding strategy to effectively and efficiently restore the breed to health.
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We have the tools and expertise to do this. We could be doing this NOW.

The Importance of Genetic Management

​The goal for every breeder is to leave their breed healthier and stronger for future generations. But without the right tools, achieving these goals can feel like navigating without a map.

The biggest challenge for breeders of purebred dogs is high levels of inbreeding and the consequences for health. We know that inbreeding has multiple deleterious effects in animals. It increases the risk of recessive genetic disorders being expressed; it causes inbreeding depression, which also affects health; and it results in loss of genetic diversity, which ultimately increases the rate of inbreeding.

Purebred dogs as a group have exceptionally high levels of inbreeding, a consequence of closed stud books that prevent the introduction of fresh genetic diversity to restore that lost over the generations. In addition, it is difficult for breeders to implement the types of genetic management strategies that would control inbreeding and loss of diversity because they simply lack the necessary information. Creating a genetic management plan requires information about the "genetic landscape" of the entire breed - not just individual dogs, or average values for things like inbreeding and kinship, but also data for the variation in these values in the population.

What's the Problem?

​Breeders are recognizing that breeding for health requires that they know more about the dogs and the breed than they did in the past. DNA testing and pedigree analysis can now provide data about the genetics of individual dogs that can be used to reduce the risk of genetic disorders in offspring. What breeders lack, however, is information about the genetic landscape of their breed. When breeders identify a potentially genetic problem, they will try to "breed around" it or remove carriers from breeding. These strategies assume that the genetic solutions they need exist in the breed and they can solve the problem by moving the breed in that direction.

Imagine you are a tourist planning a trip in a place you have never been before. Without a map, you can only navigate by guessing, and you could easily end up in the wrong place or, at the very least, waste lots of time and energy taking wrong turns and running into dead ends. If you don't have the right information, breeding decisions work the same way. Without knowledge of your breed's genetic landscape, you can't plan a path forward or determine if it's even possible to get where you want to go. 
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​The problem here is the assumption that a solution exists within the breed. Remember that recessive mutations cause problems when a dog inherits two copies of the mutation. It's not the presence of the mutation that you have to deal with, but the absence of the "wild type" (normal) version of the allele necessary for the gene to do its job. But breeders focus on mutations, and they diligently try to solve the problem through selective breeding. This takes an ongoing toll on the gene pool, ultimately increasing the risk that some other defective allele will become the next problem in the breed. You can see how this turns into a cycle of genetic whack-a-mole, damaging the gene pool with every cycle while making no progress on the actual problem. This is where we are in most breeds after decades of selective breeding, now guided by DNA tests. We have failed to improve the health of purebred dogs because we have not determined the right path to health. Without a map, we don't see a destination and can't choose a path that will get us there. We invest time, energy, and money, all with fingers crossed, hoping at least that things won't get worse. 

What's the Solution?

The solution to this problem is obvious. Breeders need more information about the genetics of their breed. Not just about one or a few dogs, but about dogs characterizing the breadth of the breed's genetic landscape. Breeders need to be able to determine - before they hit the road - that the chosen breeding path will take them where they want to go. They need also to adopt breeding strategies that will not work against them along the way. Simply removing from the gene pool any dog that has some issue, or restricting breeding to just a small fraction of the dogs produced, will perpetuate the situation we have now and foil attempts to improve it. We need to be able to identify dogs of greatest genetic value so they can be prioritized for breeding. We need to identify sires before they have litter after litter of puppies that will skew the entire gene pool in one direction and flood the breed with his unique assortment of genetic mutations. (See Pox of the Popular Sires) 

Breeders - and breeds - need is a road map of the genetics of the breed across its entire scope, so breeders can design well-planned solutions to problems. We need genetic management plans that identify a path towards a solution, instead of trying to solve problems by trying to run away from them in some random direction.

We have the information we need to create at least a basic plan for most breeds. Pedigree data and individual genotypes can be leveraged to start filling in the blank areas of the genetic landscape with useful information - where to find dogs with useful genetic diversity, where to find outcross candidates for specific dogs, which sires are overproducing at the expense of other genetically valuable dogs, and more. The information breeders need can be extracted from pedigree and DNA data and used to address the questions breeders ask when making breeding decisions. With regular updates, this information resource can display the current genetic status of both the breed and individual. It can also document the progress resulting from breeding strategies designed to reduce inbreeding and protect and improve genetic diversity.

DogsArk: The Genetic Dashboard

The good news is that we CAN get there. We can improve the health of purebred dogs without sacrificing the traits that make each breed unique. And we can do it efficiently and effectively, with tools and expertise that are available to breeders NOW. ​

ICB has built a breeder tool called DogsArk that provides the information breeders need for sound genetic management. Using either pedigree or DNA data, DogsArk provides a "genetic dashboard" that allows you to -
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• Visualize genetic diversity: Identify where genetic diversity is strong and where it is at risk;
  
  
• Track lineages and traits: discover genetic clusters and understand the distribution of traits and mutations;
  
  
• Plan sustainable breeding programs: Use real-time data to make informed decisions that preserve your breed's genetic health.

For the first time, we now have the DogsArk Breeder Tool, which will provide the information needed by dog breeders to safeguard the genetic future of their breed. With DogsArk, we can start to plan breeding strategies that will improve the health and welfare of dogs. (We are in the process of adding breeds and data, and the site is still under construction - pardon our dust!)

Have a look at DogsArk and check out the tutorial for guidance. If you have any questions or would like to add your breed to the site, just drop me an email: [email protected]

Facebook is an echo chamber of misinformation, myths, and unfounded opinions about the coefficient of inbreeding, which is unfortunate because there is probably no statistic (other than the kinship coefficient, which is related) that is more useful to breeders who want to minimize the risk of health problems in their puppies.

Here's my list of the 10 really essential things you need to understand about the coefficient of inbreeding. 
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​Livestock breeders have now realized that highly trait-specific selective breeding might improve one feature to the detriment of others that are critical to animal health. 

In milk cows,

But what we want to know is how, despite significant inbreeding depression, breeders were able to achieve such remarkable improvements in production traits? ​

In fact, commercial breeders do in fact choose the best offspring of each generation to breed to, but not just the top few animals. They select all of the best performing animals, perhaps 10-20% of the best animals. The goal is to capture the genetic variation present in the best animals. They know thatt each animal is a mix of genes from two good quality parents, and from the same parents this mix will be more fortuitous in some animals than others. The result is a collection of offspring that carry the genes of good producers, and when bred together in the next generation the new mixes of genes will once again produce some animals that are better than others. By selecting many of the top animals in each generation, the gene pool of the popualtion is gradually shifted in the direction of higher productivity as each new generation produces animals with a different mix of genes.
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This assumes that genes are at least partly responsible for the traits of interest. If not, or if the influence is very small, you will not see imprrovement in performance with seletive breeding. But as in this example of selection for a trait like speed, selection of the 10% fastest animals in each generation will move the average performance of the animals in the population to higher speed. 

Of course, not only must the trait have some genetic basis, but for this to work you need enough genetic variation to produce many new combinations of genes in the next generation of offspring, some of which can perform better than their parents. The key here is genetic varaiation. If you only keep the top animal in each generation, you will lose the genetic variation needed to improve anything. The genes associated with the best performance will become fixed in the population, ending your genetic improvement program.

​Inbreeding and strong selection eliminates the raw material - genetic variation - that is necessary for improvement of traits in animals. Because of Inbreeding in each generation of dogs, genetic variation is lost and homozygosity increases, which can drive traits to unwanted extremes. Most breeders realize that breeding together two outstanding but closely related dogs doesn't guaranted outstanding puppies. This is because loci that were heterozygous in the parents can be homozygous in the offspring, which then lose the genetic advantage of heterozygosity. This is called "overdominance", where the phenotype of the heterozygous combination is superior to the phenotypes of either allele when homozygous. For traits that depend on overdominance for the best phenotype, inbreeding will destroy the advantage of heterozygosity. 

What's the lesson here?

One of the "pearls of wisdom" often offered by long-time breeders is that you should "breed the best to the best". This suggests that the secret to success is the consistent application of this simple rule of thumb. But what we know about genetics makes clear that, while this might produce nice puppies from a pair of parents, selecting the pick of that litter and doing the same in the next generation will leave a trail discarded genetic variation that might include the raw material you need to produce something better than either parents. It's the shuffling of this variation in each generation that provides the opportunity for fortuitious combinations that can create animals that are superior to their ancestors, generation after generation. This is how we got those massive turkeys and the amazing milkers. 

Dog breeders, the value of your dogs is in their genes; it's your money in the bank that will pay dividends generation after generation. Don't toss out the lesser dogs that happened to get the perfect mix of the available variation. 

DogsArk is designed to assist dog breeders in producing genetically sound puppies while preserving breed genetic diversity. It uses essential genetic concepts, including inbreeding, heterozygosity, kinship, and fixation index, to provide insights for informed breeding decisions.

The tool is structured into three modules:

1. Breed Summary (Module A)
Overview: Offers a summary of the breed's genetic diversity, genetic disorders, and traits.

Features:

• Dog Inventory: Provides a database of dogs, distinguishing between anonymous and known dogs.
• Genetic Diversity: Summarizes inbreeding coefficients, kinship, and heterozygosity with values for each measure.
• Genotype Frequencies: Reports health-related gene statuses and frequency of normal, mutated, and heterozygous alleles.
• Body Size, Coat Characteristics, and Sex Chromosomes: Details traits related to color, texture, size, and haplotypes for mitochondrial and Y chromosomes.
• Other Traits: Lists additional genetic traits specific to certain breeds, such as brachycephaly.

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2. Genetics of Individuals (Module B)
Overview: Provides data for individual dogs on genetic diversity, relatedness, genetic “value,” and traits.

Features:

• Genetic Diversity: Displays inbreeding, fixation index, mean kinship, and heterozygosity for each dog.
• Traits & Disorders: Lists genes associated with traits and health issues, with options to filter and sort by genotypes.
• Genetic Ranks: Ranks dogs based on genetic diversity and relatedness.
• Genetic Relationships: Includes a dendrogram and heat map for visualizing genetic similarities among dogs.
• Kinship Matrix: Shows kinship levels with a color-coded heat map for assessing relatedness.
• Runs of Homozygosity (ROH): Highlights blocks of homozygosity to identify recent or historical inbreeding.
• Disease Risk Analysis: Uses a dendrogram to identify breed lines prone to specific diseases.
• Principal Components Analysis (PCA): Visualizes genetic subpopulations, helping identify genetic differences within a breed.

3. Test Mating (Module C)
Coming Soon: This feature will predict the level of inbreeding for potential litters from specific parent pairs.
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Overall, the ICB Breeder Tool is a valuable resource for breeders seeking to make genetically informed decisions, minimizing genetic disorders while fostering breed diversity. It combines scientific rigor with practical tools, enabling breeders to track and analyze genetic health trends 

Glossary of Key Terms

• Allele: One of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.
• Brachycephaly: A condition characterized by a shortened skull, often resulting in a flat-faced appearance.
• Dendrogram: A tree diagram that represents taxonomic or evolutionary relationships.
• Fixation Index: A measure of genetic differentiation among populations, often used to assess the level of inbreeding.
• Gene: A unit of heredity that is transferred from a parent to offspring and determines some characteristic of the offspring.
• Genotype: The genetic makeup of an individual organism.
• Haplotype: A set of DNA variations, or polymorphisms, that tend to be inherited together.
• Heterozygosity: The presence of two different alleles at a particular gene locus.
• Homozygosity: The presence of two identical alleles at a particular gene locus.
• Inbreeding: The mating of closely related individuals, leading to an increased chance of offspring inheriting harmful recessive traits.
• Kinship: A measure of the degree of genetic relatedness between two individuals.
• Mean Kinship: The average kinship coefficient between an individual and all other individuals in a population.
• Mitochondrial DNA: DNA located in the mitochondria, which is inherited maternally.
• Mutation: A change in the DNA sequence of a gene.
• Phenotype: The observable characteristics of an individual organism, resulting from the interaction of its genotype with the environment.
• Polymorphism: The presence of genetic variation within a population.
• Principal Components Analysis (PCA): A statistical method used to reduce the dimensionality of data by identifying principal components, which are linear combinations of the original variables.
• Runs of Homozygosity (ROH): Continuous stretches of homozygous genotypes within an individual's genome, indicating potential inbreeding.
• Y Chromosome: The sex chromosome that determines maleness in mammals.

Essential Concepts
These essential concepts are:

1) Inbreeding: probability of inheriting two copies of the same allele from an ancestor, which is called “homozygous”; it is also the fraction of genes that are homozygous. This measure of inbreeding is represented by the symbol F and is expressed either as a number between 0 and 1 (like 0.12), or as a percentage (like 12%).

2) Another way to express inbreeding is relative to the population. This is also called the “fixation index”, which is abbreviated as Fis. In a randomly breeding population, the average Fis is zero. A breeding of two individuals that are more closely related than average is considered inbreeding and will produce a positive Fis. Breeding two individuals that are less related than average is outbreeding, and Fis will be negative.

3) Heterozygosity is the fraction of genes for which the two alleles are different, so it is the opposite of homozygosity, in which the alleles are the same. Heterozygosity is represented by Ho.

4) Your relatives are your “kin”. In population genetics, we express the degree of relatedness between two individuals using the “kinship coefficient”, which is represented as the letter K.
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Okay, armed with a few key bits of information, we’re ready to have a look at the components of the ICB Breeder Tool.

The Breeder Tool consists of three modules.

1) The first module provides information about the genetic status of the breed.

​2) The second module provides information about the genetics of individual dogs.

3) The third module provides predictions of the inbreeding of a litter produced by mating two particular individuals.

The first module Indicates that you are in the Breed Summary module in the upper left corner, and the breed is shown on the right.

This module provides a summary of the genetic information about the breed, specifically the genetic diversity, genetic disorders, and genetic traits. These are organized under a set of tabs.

Dog Inventory
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​The first tab is labeled “Dogs”. It gives a quick inventory of the dogs currently in the database. It reports the total number of dogs in the data, as well as how many of those dogs are anonymous, which means that their identities are unknown, perhaps because they were part of a research study. Often, we only have basic DNA information for these data and data about genes for specific traits is not available. DNA contributed by the owner of a dog are “known” dogs, and for these we often have more comprehensive DNA information.

In this example, we have a database of 51 English Springer Spaniels. All of these are anonymous dogs and there are no dogs whose identity is known.

Genetic Diversity

The second tab provides a summary of information about genetic diversity in the breed based on the dogs in the database.

The measures of genetic diversity we use are the four we have described earlier: two types of inbreeding coefficient (F and Fis), kinship, and heterozygosity.

For each of these, the table reports the mean (or average), the median, and the maximum and minimum values.
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Genotype Frequencies

​The next tab provides information about genes associated with health and diseases.

If all of the dogs in the dataset for a breed are anonymous, there might not be data for some of the rest of the tabs in this module, and the pages will be blank (or contain place-holders).

In this particular breed, dogs are tested for the genes for alanine aminotransferase and dilated cardiomyopathy. For both of these, there are two possible alleles. The chart reports the number of dogs in the sample that have two copies of the normal alleles (they are homozygous for the normal allele), and these are labeled “clear”. The chart also reports how many dogs have two copies of the alternative allele or mutation, indicated as homozygous for that allele, and the number of dogs that are heterozygous, with one copies of both the normal and the alternative allele (heterozygous).
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Body Size

The next tab provides information about the genes associated with coat characteristics such as color, texture, or length. In this example, the K locus and E locus are genes for color.
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Sex chromosomes

The next tab reports the information about the haplotypes for mitochondrial DNA and the Y chromosome that are found in that breed. There might be many of each of these in a breed, or just a few.​

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Other Traits

​In some breeds there are genes for specific traits that are not found in most breeds, and these are under the “Other” tab. In this case, this breed carries genes associated with a shortened muzzle, a trait called brachycephaly.

For anonymous dogs, there will usually only be information under the first two tabs, for the inventory of the dogs and the statistics summarizing genetic diversity.

Module B provides the information for individual dogs about genetic diversity, relatedness to other dogs in the sample, the genetic "value" of a dog, the genes for traits and known mutations, and the genetic structure of the population. As in Module A, this information is organized on tabbed pages for navigation.
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About the Tables
Many of the tables in the Breeder Tool have filtering and sorting features. The icon of the funnel in the ICB Code column indicates that you can filter this column to just the specific animals you want to see. The other columns can sorted by ascending or descending values by clicking on the little arrow next to the column label.
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Genetic Diversity
Under the first tab, labeled “Genetic Diversity”, there is a table that summarizes the data for inbreeding, fixation index (Fis), the mean kinship, and heterozygosity of each dog. Each dog is given an ICB Code that corresponds to a key with the identity of each dog. These are the data that were used to create the "Genetic Diversity" graphs for the breed population in Module A.
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Traits & Disorders
Under the next tab is a table containing the genetic information for known genes for traits and disorders. Depending on how many genes were tested, this can be a very wide table and you will need to scroll to the side to see all of it.

You will find it very useful to filter or sort by specific individuals or particular genotypes that you are interested in.

Genetic Ranks
​The Genetic Ranks tab presents charts that rank individual dogs by the value of a particular measure of genetic diversity or relatedness. Each bar is labeled with the ID of each dog. 

Where there are many individuals in the database, the ID codes of the dogs can be difficult or impossible to read. In some cases they are readable on a tablet where you can zoom in; in other cases, you can look up the value for a specific dog and use the scale on the y-axis to see where that dog would fall on the chart.

Genetic Relatiionships (heat map)
The next tab displays a colorful map of the genetic relationships among the dogs in the database in two forms: as a family tree called a dendrogram, where the dogs that are most similar genetically are clustered together, and as a matrix called a “heat map” that compares the genetic similarity of every pair of dogs in the database. The degree of relatedness is indicated by branch length in the dendrogram, and by color in the heat map.
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Kinship Matrix
​Kinship, which is the degree of relatedness of two individuals, can also be displayed in this other type of heat map called a kinship matrix. This is similar to the heat map with the dendrogram, but in this one the dogs are not ordered. The advantage of this heat map is that the colors indicating the degree of kinship can be customized. In this one, a kinship coefficient of

6.25% or less is represented by green (equal to a cross of first cousins),

12.5% is yellow (half-sib cross), and 25% and above is red (full-sib cross). This allows you to quickly survey the levels of relatedness among animals in a population and also to identify specific levels that you might be interested in.
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Runs of Homozygosity
The next tab, labeled “ROH”, contains charts that display “runs of homozygosity” on the chromosome. These are blocks of inbreeding that are the result of inbreeding. The genome is represented by arranging the chromosomes end to end from 1 to 38 across the top, and each row is the information for a particular dog. Blue represents blocks of homozygosity of a specific minimum length. Because older inbreeding tends to get broken up into smaller blocks, we can use the ROH charts to detect recent vs older inbreeding.
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Disease Risk
​We can use a dendrogram that depicts the genetic relationships among individual dogs to explore the distribution of a particular trait or gene in the population.

For example, a research study was unable to identify a specific gene associated with mast cell tumors in Labrador retrievers. However, if we identify the dogs affected by mast cell tumors on the dendrogram, we might be able to identify lines that are predisposed to mast cell tumors. 

This technique might be useful for health issues as well as specific traits of interest.

Principal Components Analysis
​The last tab is for a graphical depiction of the genetic relationships among the dogs in the dataset using a statistical technique called “principal components analysis”, or PCA. This can be useful for identifying subpopulations of the breed that are genetically different such as show versus field lines of a breed, or varieties that differ by color.

Test Mating

Coming soon...Under construction

​The Test Mating page provides information for “predicted litter COI”, the average level of inbreeding expected in a litter produced by a specific pair of parents based on their kinship coefficient.

Let's say you're a responsible, preservation breeder (of course!), and you pride yourself in prioritizing health as a breeding goal. You carefully research pedigrees and ancestry before making mating decisions. You do all the relevant health testing (i.e., mutation testing and phenotype evaluation) for your breed. Yep, this sounds like what we want to see in a purebred dog breeder!

I'm now going to rattle your cage a bit.

What if there are things happening right under your nose that are causing significant deterioration of your breed's gene pool?  You realize that this would not be a good thing, and I'm sure you would want to know about it. Reducing the quality of your gene pool will affect breeding in every generation to follow. You rightly think this sounds like something breeders should be monitoring and mitigating if the goal is breed preservation.

One last point before you dive into the fun stuff. These mystery effects could be countering all the efforts (and time and money) you are investing in your efforts to breed better dogs. So not only is there possible damage to your gene pool, there is also a chance that your breeding program is circling the drain and you don't even know it.

What follows is one of the lessons (Module 13, unit 1) from of an online course in population genetics that I created specifically for dog breeders (ICB Managing Genetics for the Future). This unit comes rather late in the course (Module 13 of 15), so you will be missing the extensive background concepts and information leading up to this that would make it more meaningful for you. But I think you can get a lot out of it if you take the time to follow the instructions carefully as you work your way through. Think about your own breed as you do this, and I think you will see some fog clearing. Even better, throw in some numbers for your breed and see if your breed population is as healthy as you think it is.

​Above, all, have fun!

Genetic management: basic strategyThe reason we have domestic animals of particular breeds is because they are useful to us. Dogs have been put to work guarding, herding, hunting, hauling, fighting, controlling vermin, alerting, guiding, and more, and of course they have been companions as well. Breeding them deliberately allows us to produce that animals that best suit our needs through genetic selection for particular trait. Developing a breed with certain traits is essentially the process of creating a gene pool with the genetic material necessary for those traits as well as the variation necessary to improve or modify these traits as needed. Of course, if you can't breed domestic animals sustainably, your investment in their development and benefit from their use will be lost.

The development and sustainable breeding of dogs went along fine for thousands of years. Breeds that were needed were created, and those that were no longer needed went extinct. Genetic management was accomplished by doing what worked, selecting the best dogs for their purpose, culling the unfit, and finding dogs to breed to that would improve or add desired traits. Purpose and function drove selection, and the requirements that working dogs be both fit and inexpensive to keep insured that health was maintained. In the late 1800s, the purpose and means of breeding dogs significantly changed. Events originally intended for the evaluation of breeding stock turned into contests to identify the "best" specimens, then closed studbooks and "purebred" dogs were created.

This fundamentally changed the way dogs could be bred, and most significantly it removed the possibility of introducing new genes into the gene pool of a breed. The consequence has been the steady and dramatic reduction in both the genetic and physical health of these purebred dogs until we get to the situation we have today, in which the major topics of discussion among breeders are not the traits and quality of their dogs, but how to accomplish a successful breeding in the face of reduced fertility, smaller litters, high puppy mortality, and the increasing number of heritable disorders.

The health problems we have today in dogs are a direct and predictable consequence of a failure to properly manage the gene pools of the breeds. The truth of the biology is that closed gene pools lose diversity inexorably over time, and as homozygosity and homogeneity increase, health and reproductive success deteriorate. Eventually, inevitably, closed populations go extinct.

Sooner or later, if purebred dogs as we know them are to survive, the stud books must be opened and biologically appropriate methods of breeding must be allowed. Until then, breeders need to improve and protect the quality of their breed's gene pool, and in fact they will still have to do this after stud books are open.

The science of breeding and managing populations of domestic animals has developed considerably over the last 100 years, and especially in the last few decades. Genetic management strategies have been extensively explored and perfected in many kinds of animals in thousands of breeding experiments, and in fact some groups such as service dog organizations have adopted modern breeding methods that dramatically improve their ability to manage inbreeding while also producing dogs of reliable type and temperament. Breeders of all purebred dogs need to learn to do this too.

Wild animal species are closed populations too
The African elephant, Grey wolf, song sparrow, brook trout, and thousands of other familiar species of animals have been around for thousands of generations without becoming more and more inbred over time. In fact, most healthy wild animal populations have levels of inbreeding of only a few percent. How do they manage this?

Animals in a single population become inbred on each other. If you split a population, the two populations will also become inbred, but not in the same exact way. Different alleles will be lost by genetic drift, selection will be slightly different, and over several generations they will drift apart genetically. If an animal then moves from one population to the other, it can reintroduce some of the alleles that might have been lost. The ability of animals to migrate among isolated populations is how species minimize the level of inbreeding and depletion of the gene pool over time and, for the same reason, isolation of a population of animals so that migration cannot take place leads to increased inbreeding and genetic drift.


This can work the same way in domestic animals as it does in wild ones, and maintaining multiple genetic groups or lines within a breed is a useful management strategy if used properly. What this effectively does is create multiple open populations within a larger closed one.

The tradeoff is that smaller populations accumulate inbreeding more quickly and the rate of genetic drift is higher, so these things need to be taken into account when planning a breeding strategy.

Since breeding dogs aren't kept in herds or separate physical groups, these subpopulations exist on paper, and management is the process of monitoring the inbreeding and outcrossing as appropriate.

Simulating the genetics of multiple populations
We're going to use a computer simulation that will allow you to see how changes in population size, number of subpopulations, and migration rate (which for dogs is equivalent to a cross to another line) affect the genetics of the overall population.

Go to the PopGen Simulator-
http://www.radford.edu/~rsheehy/Gen_flash/popgen/

You will see two graph axes and a set of parameters you can fiddle with across the top.
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Use these settings to start:
Pop. size = 50
A1 allele frequency = 0.5
# of Populations = 1
Number of generations = 200
and leave the "Fitness" boxes all at one, migration unchecked, mutation rates both as zero, and nothing for bottleneck.

Click "Go". In the top graph, you will see that you have lines for the frequencies of two alleles, A1 and A2. Since you set A1 to 0.5, A2 will be the same at the start (because A1 + A2 must equal 1).

In the graph below, you will see lines for how the genotypes change over time. Of course, this is from the Hardy-Weinberg equation that we talked about earlier.

Leave the settings and click "Reset" then "Go" several times, and you will see that you get a different outcome every time. This is because the simulation is modeling the random inheritance of A1 vs A2 each generation. You will see that one allele or the other can disappear entirely from the population, which means the other one is "fixed" - i.e., every individual is homozygous for the remaining one.

Now, let's do some experiments and collect some data.

1) Run this simulation 10 times with the same settings and write down which allele becomes fixed and the generation (roughly) when that happens.

Change the population size to 200, and run 10 times recording the data as above.

Change the population size to 25, and run 10 times recording the data as above.

From you data, you can see that a small population is genetically unstable, and the smaller it is the more unstable and less predictable it is.

2) Change population size to 200, and change number of populations to 2. Repeat as above.
You'll see that the display changes when you do this. Now, we don't get the genotype graph, but two graphs for alleles A1 and A2, and with the two populations plotted on each. This means that the lower graph is the mirror image of the upper one, so you really only need to look at one to see what's going on.

Now, leaving those settings, click in the "Migration?" box and for rate put 0.1 (10%). (The rate values go from 0 to 1.0.)

Run your 10 simulations and note the fixed allele for both populations.

One thing you might notice is that without migration, the allele frequencies of the two populations change independently. They might both up for a while, then one goes down while the other still goes up, and so on. The allele frequencies are changing randomly. What is different when you allow migration?

Play around with the migration rate; try several values, such as 0.01, 0.25, and 0.75. As the rate of migration from one population to the other increases, do the allele frequencies in the populations become more stable or less? Are the populations more similar to each other or less?

Write a little description of your results for these experiments so you'll remember what you found as we move on.

3) Set the population size at 200, A1 allele frequency at 0.5, and now change populations to 3. Run your experiments as before.

Write a few sentences describing how the results with 3 subpopulations are different than 2.

4) In these experiments, we kept the size of each population the same (200). Now let's pretend we have 300 animals and divide them into subpopulations but keep the size of the groups equal. So you will have 1 population of 300, 2 populations of 150, 3 populations of 100, and 6 populations of 50.

We know that diving the population and allowing migration reduces the probability of completely losing an allele and the population is genetically more stable. Now, if you divide the population the simulation is more like the real world because the subpopulations will be smaller.

Run some experiments as before, and fiddle around as you wish with the same settings while thinking about your own breed - its size, subpopulations (perhaps in various countries, different kennels, or different types), and migration rate.

5) Create 3 populations of 100 animals. What is the lowest migration rate that you would need to have to keep from losing one of the A alleles from any of the populations in 200 generations when the initial frequency is 0.5?

6) If you had a population of 300 animals, and you planned to breed in a way that would result in the "migration" of 10% of each subpopulation to another one (doing this via outcrossing), how may subpopulations would you create with your 300 animals to get the best genetic stability in all of them?

7) What did you learn from this? How does the size and number of subpopulations affect genetic stability at a fixed migration rate?

8) Can you think of any "breeder myths" that you just busted with your population simulations?

You made it through this lesson. Did you learn something that changes the way you think about breeding and genetic management (or lack thereof) in your breed?

This was a single unit from a course with 15 modules, each with multiple units (averaging 3-5). Would you benefit from knowing more about how population genetics affects your breeding program? 

You can sign up to take this course here,
​https://www.instituteofcaninebiology.org/openreg-managinggenetics.html

or have a look at the other courses on offer here -
https://www.instituteofcaninebiology.org/openreg-managinggenetics.html

I do recommend that you take Managing Genetics first because it covers foundational topics necessary to understand the material in other courses.

Many breeders stress that the key to improving canine health is DNA testing and selective breeding, and many national kennel clubs and breed clubs endorse this view. However, the evidence does not support the claim that this strategy will prevent genetic disorders or even improve the health of dogs. In fact, it is easy to show why this will not work based on simple principles that any breeder can understand.

Let's say we start with a small population of healthy dogs that are not related to each other. Let's put them on an island and allow them to breed freely for many generations. Over time, individuals in the population will become more and more related to each other because of the limited number of individuals to mate with. Just by chance or through selection,  some alleles in one generation will not get passed on to offspring in the next generation and will be permanently lost from the gene pool. At the same time, unavoidable inbreeding will increase the level of relatedness among the individuals. The net effect is that some individuals will have two copies of a dysfunctional allele at a locus instead of at least one copy of of the normal, "wild-type" allele. 

The replacement of normal alleles with mutations will results in a decline in health and "vigor", including both genetic diseases and measurable traits such as reproductive success, lifespan, and survival. At this point, the population can be considered to be unhealthy, and the problem is the erosion in the quality of the gene pool.

If this was a dog breed displaying some health issues, we would assume the problem is genetics and start looking for a mutation. Sometimes one is identified, but more often the situation appears to be complex and we are unable to identify a clear cause among what we assume is a background of polygenic effects.

We have had only very limited success dealing with problems like this. There is no easy way to select against multiple unknown genes, so usually animals are removed from the gene pool. But this rarely solves the problem. New animals similarly affected continue to appear, sometimes stimulating more research to find the offending mutations. Ultimately, the solution often becomes the removea of animals from the gene pool once again.

After decades of engaging in similar strategies, breeders have not eliminated any of these problems, except where caused by a single recessive or dominant mutation. Why is this? 

We identify the problem as "bad" genes we have to get rid of. Rather, it's not the bad genes that are the problem, it is the LOSS of the normal, functional genes that should be found at that locus. They, of course, are lost through genetic drift and selection with each generation of breeding. If every unique allele in a breed's gene pool was passed on to an animal in the next generation, then the composition of the gene pool would be stable over time, and we should be able to produce healthy, quality animals generation after generation. But we don't breed in a way that protects the contents of the gene pool. Thus alleles are lost every generation, either by design or by chance. We do not protect the genes that are necessary to produce healthy animals, so as they disappear from the gene pool, we have to expect that we will see problems.

Interestingly, most wild animal populations can persist for hundreds of years, maintaining health and function because the complement of genes necessary to produce the animals is constant. How do these unmanaged populations of animals do this? It's simple. The alleles that are lost are replaced when new individuals join from other populations. This is also done deliberately in commercial animal breeding, when a single population is subdivided and managed in a rotational breeding program. This practice restores genes lost from one subpopulation through the introduction of animals from another subpopulation. A carefully run program can continue to breed in a closed gene pool for many generations, simply by preventing the loss of alleles from the gene pool. The valued traits of the animals are preserved and the health and quality of the animals are maintained at a high level. 

Note that the gene pools of ALL animals contain mutations. Why don't these mutations result in the number and magnitude of problems we wrestle with in purebred dogs? The dominant mutations are removed if they have a sufficiently detrimental effect on the animals. Others will only cause issues if paired with another copy of the mutation, because the locus for this gene will have two copies of a non-functional gene. What is absent is a copy of the normal allele necessary for a particular function. 

The problem isn't that the animal has a mutation; it's that it lacks a copy of the normal allele. Simply "getting rid" of the mutation will not solve the problem. The problem is not a malicious genetic bomb in the gene pool. It's the absence of the normal alleles that should be in its place.

What is critical for breeders to understand is that there is only ONE solution to this problem. It is to restore the alleles necessary to perform every function of the body of a dog. DNA testing will spot a few of the "bombs". But throwing those out still leaves a gene pool without the allelic diversity necessary to produce healthy animals. Every breeder knows from experience that trying to remove mutations by removing animals is fruitless; the result will not be a happy, healthy population of dogs.

Can you see that DNA testing to identify the few mutations we know about will not restore health to dog breeds? As long as the gene pool is closed, we cannot restore the gene pool to health and we will not be able to produce healthy dogs sustainably. If we want healthy dogs, we need to produce dogs with the complement of alleles necessary to support all the bits and pieces of function necessary to be a healthy dog. All breeds in a closed gene pool will already be suffering from a loss of alleles, some of which will result in loss of function. So, not only do we need to breed in a way that protects genetic diversity, we must take whatever steps are necessary to restore the diversity of the gene pools.

Our focus on DNA testing and selective breeding is failing to improve the health of dog breeds, and this is why. Advice to breeders that we can produce healthy dogs if we continue to use our current strategies is simply wrong because it suggests that loss of alleles every generation will have no detrimental effects on health and function. This is impossible.

There is lots we don't know about genetics, but there is nothing that would explain how we might continue to breed dogs as we are without the deterioration we are seeing in the health and quality of the dogs. In fact, the health issues that we wrestle with in purebred dogs are caused by the way we breed. To change the trajectory of declining health in dogs, we must change the way we breed.

The solution to our problem is obvious and conceptually simple. It has been practiced by breeders of other animals for many years. There is no magic necessary, and it's not hard. You do need good information and guidance from individuals that understand the details of population genetics in order to accomplish the genetic rehabilitation of a breed effectively and efficiently. The sooner you start, the sooner we can be dog owners and breeders without also being experts in cancer, epilepsy, kidney failure, or sudden cardiac death.

Finally, the average dog lover is growing intolerant of the high incidence of health problems in purebred dogs. They identify the breeders as part of the problem, and they are not wrong. Pressure on breeders to improve health doesn't seem to be resulting in significant improvement, so the impetus now is legislation that will regulate dog breeding and make it illegal to produce animals that can be expected to suffer from health issues. 

Breeders have experience in dog breeding. We must pair this with expertise in the proper genetic management of animal populations. To restore dog breeds to health, we must encourage and support this essential partnership. 

Fueled by concerns about the health of purebred dogs, and supported by the growing list of mutations known to cause genetic disease, there has been much discussion about whether purebred dogs are predisposed to health issues compared to dogs that are not purebred.

The latest addition to the discussion (Forsyth et al 2023) is a study coming out of the Dog Aging Project, which took advantage of a large database (27.5k dogs) including both mixed and purebred dogs with extensive information about the health and welfare of each individual.

The project summary states that "purebred dogs...did not show higher lifetime prealence of medical conditions compared to mixed breed dogs". Furthermore, "a higher proportion of purebred dogs than mixed-breed dogs had no owner-reported medical conditions".

In the purebred dog community, this was hailed as a decisive nail in the coffin of the "myth" that mixed breed dogs are healthier than purebreds. There was what I would characterize as glee in what they saw as confirmation of what most breeders have long asserted, despite warnings from the scientific community (and some smaller groups of breeders) that inbreeding is detrimental to health in dogs, just as it is in humans and other animals.

I was very interested in this paper, given that the information available to date supports the notion that inbreeding is detrimental to health. This study seems to present information that flies in the face of the expectations about dog health that come from an understanding of the genetics of animal breeding. So I gave it a careful review.  ​

Motivation of the study
The authors recognize that inbreeding in purebred dogs increases the risk of expressing genetic disorders produced by recessive mutations. This leads to the expectation that purebred dogs are more likely to be afflicted by genetic disorders than mixed breed dogs. However, they note that this is not always the case, and that "simpy being purebred may not necessarily be associated with increased disorder prevalence overall" (Forsyth et al 2023).

From this, they describe a study with goals to "estimate the lifetime prevalence of medical conditions among US dogs", and to "determine whether purebred dogs have a higher lifetime prevalence of specific medical conditions compared to mixed-breed dogs".

But the central question - are mixed breed dogs healthier than purebreds - remains an important one. Indeed, it critical to the defense of breeding within a closed gene pool, and justifying the high levels of inbreeding that result.

​So here's the deal. We understand the science, so we understand why mixed breed dogs should be healthier than purebreds - if we consider disorders caused by single recessive mutations. (Read more about this HERE). Indeed, this science is the reason that most available DNA tests are for disorders caused by single recessive mutations. The science tells us why these things are true. If it happened that purebred dogs were LESS likely than mixed breed dogs to suffer from genetic disorders, then we would have to conclude that we don't have the science right, and there would be lots of scrutiny to figure out why we're wrong.

​But all indications are that we DO have the science right. If somebody is trying to claim that purebred dogs are just as "healthy" as mixed breed dogs, you can know for a fact that they are not referring to recessive genetic disorders, or they are ignorant of the science.

REFERENCES
​
Forsyth et al., 2023. Lifetime prevalence of owner-reported medical conditions in the 25 most common dog breeds in the Dog Aging Project pack. Frontiers in Veterinary Science 10: 1140417. DOI
​10.3389/fvets.2023.1140417

To learn more about the genetics of dogs, check out
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By Carol Beuchat PhD

In any discussion about crossbreeding (mating two different breeds), somebody will surely claim that the offspring will be afflicted with the diseases of both breeds, or at the very least new mutations hiding in the gene pool will wreak havoc in future generations.

​Is this true?

The best way to reduce the risk of genetic disorders caused by recessive mutations is to avoid breeding related dogs, which is a problem in a closed gene pool where everybody is related. Because purebred breeds have been bred within a closed gene pool for many generations, the dogs within a breed will share many mutations, but the dogs in different breeds will not. If you are crossing Breed A with Breed B, and the breeds are not closely related (e.g, Wire and Smooth Dachshunds, English and American Cockers), then the risk of producing a disease in the puppies caused by a recessive mutation will be equal to the kinship coefficient of the pair of dogs, which tells you how genetically similar they are. (The coefficient of inbreeding of a dog is the kinship coefficient of its parents.)

So, if a breed cross will produce pups with predicted genomic COI of 2%, then the risk of producing puppies with two copies of the same recessive mutation is 2% - extremely low. As far as genetic disease goes, a breed cross has a very low risk. And because you understand the genetics of dominant and recessive alleles, you know that the risk of the introduced mutations causing a genetic disorder somewhere down the line will stay very low as long as the mutation is rare in the population, AND you avoid breeding to closely related dogs.

So, introducing new recessive mutations to a breed from crossbreeding won't be a problem unless you break both of Mother Nature's Breeding Rules:

1) Don't make a bunch of copies of a mutation and spread it throughout the gene pool. (Popular sires, we're pointing at you).

2) Don't breed to your relatives.

Get those two things right, and crossbreeding isn't a problem.

In fact, think about this - it is far riskier to breed within a closed gene pool than to crossbreed to an unrelated breed. Some breeders will claim that they won't crossbreed because "they know what's in their lines". How could they if the "bad genes" are recessive and therefore silent? So, you can reject this claim out of hand because it is inconsistent with what we know about genetics. 

If we stick to science, and ignore the arguments and excuses coming from hearts instead of heads, then crossing two breeds will not in fact produce a litter of puppies that is riddled with disease. You might not care for the conformation or other qualities of the puppies, but they will be spared the genetic disorders resulting from inbreeding that normally afflict the breed.

Next time you're at a party with your friends in the dog fancy, grab your favorite adult drink, and when there is a lull in the conversation, boldly claim that crossing two breeds is much less likely to produce genetic disorders in the puppies than inbreeding. Then just sit back, relax, and enjoy your drink.

Once again, it's time for the yearly pilgrimage to New York for the prestigious Westminster Kennel Club dog show. The airports have an unusually high number of dogs relaxing in the waiting areas, tended to by owners and handlers that look after their every need. It's a big event attended by the elite in the US dog world, and it  attracts a large public attendance as well as national television coverage.

There is no shortage of information about genetic disorders in dogs (Google, of course), and quite a bit about what needs to be done to improve things. Yet here we are again this year, off to an event that celebrates the beauty and function of the purebred dog, and where we will avert our gaze from the genetic issues that slowly erode away the DNA coding that produces every individual of every breed. 

I will be watching the WKC Kennel Club dog show this year, to enjoy the beauty and incredible diversity of this remarkable animal, the dog. But once again, I will worry about whether we will heed the warnings of the biologists and breeders of other domestic animals that, with every new generation, we are gambling with the future of a breed by putting short term gain before the obligation to breed in a way that protects the unique genetic package that defines the essence of each breed.

Breeders want to produce puppies that are healthy, long-lived, and have the type and traits that define the phenotype and behavior of the breed. The main tool used to guide breeding decisions is the pedigree, which records the history of the dogs in the breed. This can be paired with health and trait information to select dogs for mating that are likely to produce the desired offspring.

This is how we have bred purebred dogs for more than 100 years. In the last decade, the development of DNA tests for specific genes has allowed breeders to "see" what they're doing, allowing selection of dogs that have specific genes for traits as well as those carrying deleterious mutations, taking some of the guesswork out breeding for phenotypic traits like coat characteristics (color, long or short, straight or curly, etc) or body size, as well as an ever-increasing list of mutations associated with diseases or disorders. 

Breeders are familiar with the standard 5 (or more) generation pedigree chart that shows ancestors of a specific dog. However, most breeders are not familiar with the treasure trove of information that can be extracted from a pedigree database. Here are some of the statistics about a breed that can be extracted from a pedigree database and which should be part of every breeder's toolbox for proper genetic management. These terms are "jargon" and likely unfamiliar to you - and they go by somewhat nerdy names - but fear not. Keep the definitions in front of you for reference, and look up definitions as necessary when you review the data for your breeds or others. 

To make the best possible breeding decisions, breeders should have these tools in their tool box. 

Effective number of founders (fe)
Most breeds go back to a small population of "founder dogs", those individuals that contributed to the allelic variation in the original population. The genes in these founders define the size of the original gene pool. However, some of this original diversity is lost over time due to genetic drift (random chance) and selection, so the current population's gene pool will be smaller.

To estimate the size of the current gene pool, we can compute the "effective number of founders" (fe). This is an estimate of the number of founders that would produce the current genetic diversity of the population if all contributed equally to subsequent generations. This is a measure of the fraction of the genes contributed by the founders that still remain in the population. Alternatively, it represents the fraction of the original genetic diversity of the breed that has been lost due to genetic drift or selection.

Founder genome equivalents (fg)
This is the number of hypothetical founder dogs that could produce the same genetic diversity of the current population if each founder contributed equally and there was no loss of founder alleles through genetic drift. 

Effective population size (Ne)
Effective population size is the size of an "ideal" population of animals that would have the same rate of inbreeding, or decrease in genetic diversity due to genetic drift, as the real population of interest. It is not the same as census size, which is the actual number of individuals in a population. Ne reflects the "genetic size" of the population in that it depends on the number of animals that are breeding, which will always be less than the census size of the population. The rate of inbreeding in a population increases as Ne get smaller, so it tells you about the "genetic behavior" of the population in terms of how fast inbreeding will increase in the future. For a sustainably breeding population, the value of Ne should be at least 100, and some recommend at least 500 (the rate of inbreeding will be slower with higher Ne).

Equivalent Complete generations (EqG)
This is an estimate of the completeness of the pedigree database you are using. Missing data will reduce EqG and result in underestimation of inbreeding calculated from a pedigree database. A more complete pedigree database will have a higher EqG. 

These five statistics computed from a pedigree database should be available for every breed as the basic tools that can be used to offer insight into the present genetic status of your breed. The are fundamental to genetic management plans to control inbreeding (and therefore genetic disease) as well as mating strategies to protect genetic diversity. Instead of flipping through piles of printed pedigrees trying to estimate inbreeding and relatedness of individual dogs, these statistics provide quantitative information that can help you make the best possible breeding decisions. 

 Here are some examples of these statistics for a variety of breeds (from Mabunda et al 2022).

A quick look at these data can tell you about the genetic status of each breed. For example, the Finnish Spitz has the most complete pedigree database of these breeds (EqG = 10.88), so the statistics for this breed will be more reliable  than for other breeds with lower EqG. The inbreeding coefficient (F) for the Finnish Spitz calculated from the pedigree data is 6.33%. As explained above, this is much lower than the inbreeding coefficient determined from DNA (F = 28.5; Bannasch et al 2021). The ratio of fe/fa (1.5) indicates a loss of some of the genetic diversity that was present in the founder population. The values of Ne range from 384 (Ca de Bestiar) to only 3.2 (Bouvier des Ardennes), and the value for Finnish Spitz is 75.53. 
​
​Ne can be increased by balancing the number of male and females used in breeding. Since fewer males are used than females in most breeds, the simple solution to low Ne is  increasing the number of males used in the breeding program.

The data for these breeds can give you an idea of the genetic health of each breed. Some have small founder populations (e.g., fe = 3; based on the pedigree data), and only two populations have gene pools greater than 100 (fe = 117 and 205.5, for Border Collies in Hungary and Australia, respectively). Some breeds have dangerously low Ne (Bouvier des Ardennes), some have experienced a significant bottleneck (Border collie, Hungary), high inbreeding (36.45% and 44.7%, for Czech Spotted dog and Bouvier des Ardennes, respectively.

This information about a breed can give you a "heads up" spot check of a breed's genetic health. Having a large population size can be very misleading, but beyond the number of dogs and maybe an underestimate of the inbreeding coefficient, breeders do not have the basic information about the genetics of the population that is summarized here.

These statistics are essential tools that should be in the breeder's toolbox. Of course, every breed should have a good pedigree database, and if yours doesn't already this should be motivation to remedy this. If you do have a good pedigree database, these statistics can be computed for your current breed population, and refreshed to reveal the consequences of breeding decisions on genetic health.

If your breed does not have a good pedigree database, urge your fellow breeders to work on this. The database should be global and should go back as far as possible. 

With a pedigree database in hand, I can generate the statistics I describe here to provide the first window into the current genetic status of your breed. If you are breeding for preservation and health, this information is essential.

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

Mabunda et al 2022 Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review. Diversity 14:1054. https:// doi.org/10.3390/d14121054.

To learn more about the genetics of dogs, check out
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By Carol Beuchat PhD

I am often contacted by breeders that are concerned about inbreeding and loss of genetic diversity in their breed. They recognize that these things matter over both the short and long term, and that they affect the burden of genetic health issues in the breed. The question from the breeder is "What do we do about this?"

Invariably, they bring up the issue of what dogs they should cross to, either individuals in the breed, or other dogs that are completely unrelated (e.g., another breed, mixed breed, etc.)

Breeders always want to discuss this right from the start. But, for a genetic rehabilitation project, you need to identify the specific problems you need to solve before you make decisions about what to do. The "What do we do" questions will get answered after we first ask "What are the genetic problems that need to be solved?"

Genetic analyses, whether from pedigrees or DNA, will produce information containing a bunch of terms you are probably not familiar with. To use this information, you will need to understand the vocabulary and what the data produced can tell you. Do not think you can learn this stuff from chats in Facebook groups. If you're going to put in the time and make an investment in doing these analyses for your breed, please take the ICB online courses. I am not aware of any other educational resources that are developed specifically for dog breeders and that cover the essential information while requiring no background in science. You need to invest some time in your own education or you won't know how to use the information from data analyses. Remember, the goal here is to figure out what breeders need to do to solve specific genetic problems in the breed. For this, you will need to understand the information provided. Take the courses. 

I have created a table (below) with some information about the types of basic information that you can extract from both pedigree data and genotypes. In general, I would advise breeders that only intend to use data from one of these sources to use pedigrees. It might seem that DNA should be better because it uses "high tech" techniques to provide information about chromosomes and genes. But, in fact, you will find that a pedigree analysis provides all the information you need to do a good job of genetic management of a breed. It requires no effort (or cost) from breeders to keep it up to date, and it will provide critical information for you generation after generation, forever. There is some overlap in what can be extracted from pedigree versus DNA data, but pedigrees might be better for some things and DNA better for others. Again, if you have the option of doing both, that is the most useful thing to do.

If you want to use DNA genotype data for your breed, you should use SNP (single nucleotide polymorphism) analysis, not microsatellites (or single tandem repeat markers, STR). Embark uses the most popular, research grade analysis based on high-density SNPs. Their output can be combined with data produced by any research lab using the same chip (e.g., data from a study). Wisdom also uses SNPs but they have a lower resolution chip of their own design and their data cannot be combined with Embark's. Also (and more importantly) they do not make the genotype data available to the user, so third-party analysis (as I am describing here) is not possible. Microsattelite data cannot be combined with SNPs, and they do not provide the resolution needed for planning a genetic rehabilitation program for a breed. However, STRs can provide data for the genes for the immune system (DLA, dog leucocyte antigen), and this is useful to know so you can breed for high diversity in these genes specifically.

The table below includes some additional information about the convenience and logistics of obtaining and managing data from pedigrees versus DNA genotypes. 

Armed with the information from analysis of your pedigree database or DNA genotyping, you are ready to start summarizing the issues that need to be addressed. For this, you will also need to know some other things - the actual number of living dogs, how many of these can be used in a breeding program (i.e, not spayed or neutered), and how many breeders there are and where they live (e.g., country). This is also the time to pull out all the information you have about phenotypic traits that you care about (e.g., coat color, variety, etc.) as well as known health issues and associated genotypes when known.

All of this is information that should be available about your breed anyway, but usually the motivation for getting things together is the realization by breeders that there are issues about genetic health that need to be addressed. With some information extracted from pedigrees or DNA genotypes, we can take a lot of the guesswork out of making breeding decisions. A little effort invested now in data preparation will yield benefits for the breed far into the future.

I have provided the reference for a nice paper by Mabunda et al (see References) about using pedigree and molecular data to evaluate genetic health of dog breeds. It contains a useful summary of the information provided by pedigree and genotype analyses and how to use it. You will see some jargon that might be new to you, so you can start here to become familiar with meanings and concepts. There is much more to know about how to set up a genetic rehabilitation program for your breed, but this is the place to start.

If you would like to know more about the genetic status of your breed and what can be done to improve it, contact me and we can discuss where to start.

When you select a pair of dogs for your next litter, one of the things many breeders consider is the level of inbreeding expected in the resulting puppies. Most recognize that "lower is better", but how low, and better than what? If you poll a group of breeders, some will respond that inbreeding should be kept less than 5%, or less than 10%, but what's so special about those numbers? Is 5% fine but 6% is not? Is 10% okay, but 12% death and destruction?

To address these questions, you must know what the coefficient of inbreeding (COI) is and what it tells you. (Here and elsewhere, I always mean the actual level of inbreeding, as you would get from genomic DNA or a pedigree database that is complete back to founders.) 

The inbreeding coefficient was originally devised to give animal breeders a way of estimating the degree inbreeding in their stock. But what is inbreeding? Animal breeders figured out long ago that if you repeatedly bred related animals together, the quality of the offspring began to decline, something they termed "loss of vigor". They knew that a cross with an unrelated animal restored normal vigor to the animals. What they needed was a way to determine the level of inbreeding in their animals so they could determine the "tipping" point,
in the tradeoff between benefits and costs of inbreeding. In populations of animals with complicated pedigrees, it could be difficult to do this. What was needed was a way to derive inbreeding quantitatively based on the relationships of the animals in the pedigree.

The coefficient of inbreeding was devised specifically for this purpose. If an animal inherits two copies of an allele that is passed on down both sides of a pedigree from a common ancestor, this produces homozygosity at this locus. This specific form of homozygosity, where two copies of the same allele are "identical by descent", is the definition of inbreeding.

The inbreeding coefficient reflects the fraction of loci that are homozygous because of two copies of the same allele were inherited from a single ancestor. (It is also the probability that a specific locus will have two copies of the same allele inherited from a common ancestor.)

By definition, inbreeding is the inheritance of two copies of the same allele inherited from a common ancestor, so this risk should be zero if there are no shared ancestors in the maternal and paternal lines. However, if the parents are related, they will have some genetic similarity, and the more closely the relationship the greater the similarity. So from the breeding of unrelated dogs, which would produce a COI of 0%, to increasing degrees of relatedness of the parents (e.g., distant cousins, near cousins, nephews, half-siblings, etc), you would expect to see an increasing level of inbreeding, i.e, the fraction of homozygous identical alleles. For example, a cross of first cousins results on average in a COI of  6.25% in the offspring. Mating half siblings produces inbreeding of 12.5%, and crossing of full sibs results in 25% inbreeding. You can get even higher levels of inbreeding if the parents themselves are inbred, as you might see with consecutive full sibling crosses generation after generation.

So here's the burning question: Why do we need to worry about inbreeding? What exactly is the problem caused by homozygosity of alleles that are identical by descent?

The first thing you need to understand is that nature favors heterozygosity over homozygosity. Imagine a gene with multiple variants (alleles), each of which confer some different degree of resistance to a bacterial infection. Those with the alleles providing the least resistance might get sick and die, those with the best resistance will survive infection with little negative effects, and animals with a third allele might get sick and survive, but with lower fertility. The allelic diversity in the population of animals prevents entire populations from being wiped out. The animals that survive are more likely to have the alleles that conferred partial or complete resistance, and the population is better able to survive this bacterial infection in the future. 

But what if there is lots of inbreeding in the population? Many individuals might have the same allele, and for some that allele could even be homozygous. If it happens to be an allele that confers resistance, the population will be fine. But otherwise, the population will take a hit, with reduced reproduction or even death of animals with the other alleles. 

This is a simple example, but you can image a similar situation for many genes in the genome of a animal, which will be reflected in the allelic diversity of the population. Individuals in healthy populations of wild animals usually have an inbreeding coefficient in the very low single digits, even 0%. 

These two charts (below) depict the individuals chromosomes of a wolf (left) and a German Shepherd dog (right) (Wang et al. 2012). The regions on each chromosome that are "low diversity regions" (LDR; i.e., homozygosity) are in dark blue. It is easy to see that the German Shepherd has much more dark blue, indicating regions of homozygosity. A population of wolves like this one with low inbreeding is more likely to have the allelic variation that will allow it to adjust to variations in the environment than a population of inbred Germans Shepherds that has much less allelic variation. This effect is so strong that it tends to keep inbreeding levels of wild populations extremely low as long as the population is relatively large and there is some exchange of individuals from other packs. 

Mother Nature prefers heterozygosity, because inbred individuals in a population are less successful. But just how picky is she?

This is the question often voiced by breeders: What level of inbreeding is "safe"?

To address this question, we can look at data for effects of inbreeding on "fitness", i.e., traits that reflect the ability of the animal to grow, reproduce, and survive.
​

Longevity
Thanks to the tendency of royalty to marry their relatives, we have interesting data for humans on the effects of inbreeding for various traits. One such dynasty was the Spanish Habsburgs, for which we have data for various parameters of interest (Alvarez et al. 2011). These are data for survival of children to at least 10 years of age as a function of the degree of inbreeding estimated from pedigrees. Children with the longest lifespans had inbreeding levels less than about 6%. Above this, survival to 10 years dropped sharply, with less than 50% achieving this age. 

There are similarly dramatic effects of inreeding on lifespan in dogs. ​In Standard Poodles, dogs with inbreeding less than 6% live longer than those with higher COI. The penalty paid for an increase in inbreeding from 6.25% (first cousins) to 12.5% (half sib mating) was about 4 years! At 8 years old, more than 80% of dogs with low inbreeding are alive, while only 60% of dogs with inbreeding > 6.25% survived to this age. In dogs with low inbreeding (< 6%), 80% survived at least to 12 years old; only 30% of inbred dogs survived to that age.

​There is a similarly dramatic effect of inbreeding on lifespan in Bernese Mountain Dogs, many of which fail to live beyond 6-9 years old (Klopfenstein et al 2016). This chart (Long & Klei, Bernergarde) shows that each 10% increase in COI reduces lifespan by 200 days. That is, lifespan is reduced by 20.6 days for each 1% increase in inbreeding (Long & Klei, 2009).  For a dog with a COI of 30%, that's a reduction in lifespan of almost two years.

​The effects of inbreeding on longevity have been compiled (Leroy et al 2014) for a group of breeds that include Bernese Mount Dog, Basset Hound, Cairn Terrier, Epagneul Breton, German Shepherd Dog, Leonberger, and West Highland White terrier. This chart shows longevity of each breed at three levels of inbreeding, with signifiant effects indicated by asterisks.
​

​Consequences of inbreeding can be manifested at a very early age. These data for Beagles show that there is more than 20% mortality of puppies at 10 days of age at COIs up to 25%. (The data from 0% to 25% are pooled, so we can't determine how mortality was affected by inbreeding levels less than 25%). As inbreeding increases above 25%, the mortality increases significantly, to about 30% for dogs with COI between 25-50%, and about 50% for inbreeding of 50-67%.

Reproduction
Inbreeding reduces reduces fertility and effective length of reproductive period in humans (Alvarez et al 2015).
​

Inbreeding affects various aspects of reproduction in dogs as well. ​These are data for litter size as a function of inbreeding coefficient for six breeds of dog from the Swedish Kennel Club database. The top graph is litter size in number of puppies, the graph below is the decline in litter size from the value at the lowest level of inbreeding (litter size as a 5 of maximum), so all breeds start at 100% and decline from there.

These are data from the same study of longevity by Leroy et al. mentioned above. The data show that higher levels of inbreeding in both the dam and the litter negatively affect litter size. (Leroy et al 2014).
​

A recent study (Chu et al 2019) has taken advantage of the data from the Golden Retriever Lifestudy sponsored by Morris to show that inbeeding reduces litter size in Goldens. The average level of inbreeding in 93 dogs used in the study averaged 31.6%, and ranged from 18.7% yo 49.9%. A quick look at the levels of inbreeding in the various studies mentioned above makes clear that the inbreeding in these Goldens is extremely high, with all individuals higher than the 12.5% COI that would result from a cross of half siblings. While they did find a negative effect of inbreeding on litter size, note that we would expect to see a substantial reduction in litter size over the range from 0% to 20%, for which they have no data.
​

Diseases
The detrimental effects of inbreeding can be manifested as increased incidence or risk of disease.

In humans, inbreeding increases the prevalence of multiple disorders including cancer, Schizophrenia, and epilepsy Alvarez et al 2011). In the chart below, asterisks indicate significant difference from the prevalence at the lowest level of inbreeding (0.6%). Note that the highest level of inbreeding in these data is only 3.6^%, far less than we would be worrying about in a dataset for purebred dogs. It's also clear that the relationship between prevalence and inbreeding appears to be roughly linear, potentially allowing prediction of disease incidence at much higher levels of inbreeding. 

You have seen here some actual data for the effect of inbreeding on various traits in humans and dogs. Based on this, what level of inbreeding would you argue is "safe"? Truth is, we need to define "safe". If by this we mean there are no deleterious effects of any sort, the answer is clearly 0% - in general, NO level of inbreeding is without negative effects. Furthermore, the effects of inbreeding on quantifiable traits or diseases is generally linear; that is, as inbreeding increases, the magnitude of inbreeding depression (the negative effects) on a trait increases in proportion. There is no "5% threshold", below which inbreeding is "safe", nor is there a 10% cutoff above which there are horrible consequences. The effects of inbreeding on individual animals with the same  COI will vary (because no dogs are genetically identical and each will have it's own pattern of homozygosity), but across a range of inbreeding levels, the effect will be linear.
​
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What else?

I have pulled out data above for humans and dogs because I could find examples of data for both and the particular traits are familiar to breeders.

But don't think that the scanty data presented here is flimsy justification for arguing that we do need to worry about the negative effects of inbreeding, even at very low levels. In fact, there are mountains of data for the consequences of inbreeding in livestock and other domestic animals, because the profitability of commercial breeding hangs on getting the best level of inbreeding to balance benefit with detriment.

​This takes us back to the livestock breeders we mentioned above. They recognized that there were some benefits produced by inbreeding, including more predictable, consistent traits in the offspring. But they also realized that more of a good thing didn't make things even better. Breeders needed a quantitative estimate of inbreeding so they could know the level of inbreeding at which the costs began to outweigh the benefits. Hence, the development of the coefficient of inbreeding. They explicitly embraced the realization that there were negative consequences to inbreeding, but in some instances the risk might outweigh the particular negatives. ​With a way to estimate COI for any animal and any potential cross, and data for how the traits they were interested in were affected by increeding, they could fine tune their mate selection to have the greatest likelihood of maximizing benefit relative to detriment.

This is a table of data for effects of inbreeding on various traits for dairy cattle, using inbreeding estimates from both pedigrees and genomic data (Gutiérrez‐Reinoso et al. 2022). The numbers are the regression coefficients for the slope of each effect when graphed on level of inbreeding. This is the "inbreeding depression" indicated in the graph just above (right) as the slope of the line on of the trait on inbreeding coefficient. With data like this, a breeder could figure out what level of inbreeding will provide the most benefit with a tolerable detrimental effect.

To be able to do this, they have carefully collected the trait data to use in an analysis like this from thousands or even millions of animals over many generations. Dog breeders are not likely to do this, but the point is that we are entirely casual about inbreeding, and we should assume that just because we don't have the data to show that there are deleterious effects doesn't mean there aren't any. Notice also that this paper considers both pedigree and genomic estimates of inbreeding, and advocates that breeders should use both to get the best information to use in breeding. Notice that with data like this, they can estimate the effects of very small differences in levels of inbreeding on a trait, even as little as a 1% increase in inbreeding coefficient.

What level of inbreeding is "safe"?
From the information presented here, it is clear that inbreeding at any level has consequences, and that even very small changes can be relevant. In a litter of puppies, no two puppies will be genetically identical, so even if they have the same level of inbreeding, the homozygosity will likely be at different loci on the chromosomes. So you can have a puppy with 5% COI that is robust and healthy, and another also with 5% inbreeding that happened to be homozygous for loci that produced a negative effect. For this reason, COI is not an index of "health". It is a prediction or estimate of homozygosity, and that homozygosity might be either good or bad. But we know that in general, homozygosity has deleterious effects and should be avoided when possible for that reason. The bottom line is that NO level of inbreeding is "safe" or without consequences. 

If there are negative effects of even very low levels of inbreeding on a wide variety of traits, you might assess the inbreeding levels of your own breed with a new perspective. Knowing what we do now, these data for dogs should be shocking. Livestock breeders worry about single digit increases in inbreeding, and begin to panic when inbreeding increases above 6%. The data for dogs show that most breeds have an average level of inbreeding higher than a population of half-sibling crosses (the yellow line), and about 60% of breeds are even higher than the level for a full-sibling cross (red line). From data for other animals, we should expect that dogs should suffer from reduced fertility, shorter lifespan, higher puppy mortality, greater risk of genetic disorders, blood and immune system disorders, and many other things that we aren't even aware of.

Find the data for your breed on the charts below. If your breed is not on the first set of graphs, download the file just below labeled "Bannasch et al 2021", which contains some additional breeds.

If your first response on finding the data for your breed is to assume that the data must be from some non-representative population, because "inbreeding in my breed is nowhere near that high", I can assure you that these data are indeed representative of your breed. These are averages of a sample of dogs, so some individual dogs will have lower than average inbreeding, but at the same time some individuals will be higher. The point is that the livestock breeders try to keep inbreeding lower than about 5%, because at levels higher than this the detrimental consequences of inbreeding outweigh the benefits. These breeders demonstrate that you can have levels of uniformity and consistency in a group of animals at very low levels of inbreeding, so it is simply not the case that (as often claimed by dog breeders), high inbreeding is necessary to "fix type" produce consistency. This is nonsense. We CAN have both health and breed quality, but not at the levels of inbreeding typical of most purebred breeds. 

Breeders that are serious about preservation of their breeds will recognize the fix we're in right now and take steps to remedy a really bad situation. It is possible to accomplish genetic "rehabilitation" of a breed, to restore it to health and preserve the traits that make each breed unique. 

But this will require these breeders to step out of the bubble of ideology and misinformation that has justified ridiculous and completely unnecessary levels of inbreeding, and use the tools and information of science to return to breeding strategies that maintain type without compromising health. 

​There are additional data in the paper by Bannasch et al that I have displayed in this graph (below).

REFERENCES

Alvarez et al, 2009. The role of inbreeding in the extinction of a European royal dynasty. PLoS ONE 4:e5174. doi:10.1371/ journal.pone.0005174.

Alvarez et al, 2011. Inbreeding and genetics. Advances in the study of genetic disorders. 

Alvarez et al 2015. Darwin was right: inbreeding depression on male fertility in the Darwin family. Biol. J. Linnean Soc 114: 474-483.

​Armstrong JB, 2000. Longevity in the Standard Poodle. The Canine Diversity Project.

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

Charlesworth & Willis. 2009. The genetics of inbreeding depression. Nature Reviews: Genetics 10:783-796.   doi:10.1038/nrg2664

Chu et al 2019. Inbreeding depression causes reduced fecundity in Golden Retrievers. Mammalian Genome 30: 166-172. https://doi.org/10.1007/s00335-019-09805-4.
 
Klopfenstein et al 2016. Life expectancy and causes of death in Bernese mountain dogs in Switzerland. BMC Veterinary Research 12: 153. DOI 10.1186/s12917-016-0782-9.

Leroy et al 2014. Inbreeding impact of litter size and survival in selected canine breeds Vet. J. 203: 74-78.

Long P & B Klei, 2009. Inbreeding and longevity in Bernese Mountain Dogs.

Gutierrez-Reinoso et al 2022. A review of inbreeding depression in dairy cattle: current status, emerging control strategies, and future prospects. J. Dairy Research 89: 3-12. doi.org/10.1017/ S0022029922000188.

Rehfeld 1970. Definition of relationships in a closed Beagle colony. J. Am. Vet. Res. 31:723-732.

Wang et al 2012. The genomics of selection in dogs and the parallel evolution between dogs and humans. Natre Communications 4:1860. DOI: 10.1038/ncomms2814.

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We are entering a new time as residents of earth. As of a few days ago, we are breaking global heat records every day, and this will continue for the forseable future. Just yesterday, a biker in California stopped to help a group of overheated and dehydrated hikers, and while they all made it home safety, the hero biker died. 

Here is a very timely publication with FACTUAL information about how to respond to heat stress in dogs. It debunks some of the common, but incorrect, recommendations you have probably heard. We need to displace those incorrect suggestions bouncing around on the internet with FACTS and DATA. 

Read this paper. Share it with your friends with dogs. 

The key information:

"​Heat-related illness (HRI) is a potentially fatal disorder that can occur in dogs following exercise or exposure to hot environments. While many risk factors can affect the probability of HRI occurring, the priority for treating dogs with HRI is early and rapid reduction in their core body temperature to limit disease progression. Cold-water immersion (conductive cooling) and water spray with air movement (evaporative cooling) are the recommended treatments for dogs with HRI, with cooling attempts in dogs with HRI being strongly advised to take place prior to transportation for veterinary care."
​

Neonatal mortality is a significant problem in dogs, with rates generally averaging from 5-30% (Gill 2001; Tonnessen et al 2012). After eliminating individuals with developmental abnormalities or other apparent issues, most of this mortality is due to uterine inertia, in which the strength and frequency of contractions are not sufficient to expel the puppy. This results in protracted labor, with the result that puppies run out of oxygen before birth, resulting in stillborn puppies that die of asphyxia. Some puppies are born live but physiologically compromised as a result of hypoxia during parturition; these may die in the days or weeks after birth.

The data in the table below are for the disposition of 2,574 puppies of 44 breeds that were produced by 125 breeders in Australia from 1991 to 1998 (Gill 2001). Most of the mortality in this cohort (61.5%) was due to puppies that were stillborn or died in the first 24 hours. About 65% of whelpings required no assistance for delivery, while dystocia occurred in 35.6%. Emergency cesareans were necessary for 18% of the litters. In 48.6% of the litters, there were no mortalities; 14.8% of litters had stillbirths, and in 6.6% the entire litter died, although about half of these were singleton litters.

The charts below show data compiled from the records of the Swedish Kennel Club for 58,439 puppies from 10,810 liters whelped in 2006 and 2007 (Tonnessen et al 2012). The data are reported as 1) puppies that were stillborn and 2) as perinatal mortality (the percentage of all puppies born that did not survive past 7 days, including stillbirths). (Only breeds with data for at least 10 litters.)

What is evident in these data is the wide range of values across breeds. There are a few breeds in which stillborn or perinatal mortality is very low or did not occur in this sample (e.g., Basenji, German Spitz). But for most breeds, it is clear that puppy mortality is unacceptably high, even greater than 10% in many breeds.

The exceptional rates of mortality in puppies have been a significant veterinary concern for several decades. While attributed to uterine inertia, the cause of uterine inertia has not been determined. Suggestions include uterine fatigue, over-stretching of the uterine muscle (e.g., from large litters), and inadequate levels of oxytocin. Treatment of uterine inertia generally involves administering calcium or oxytocin, although these have either limited effectiveness or none at all in improving uterine contractility and expulsion of puppies (Bergstrom et al 2006; Prashantkumar & Walikar 2018).

The relative rates of mortality of puppies might seem low (i.e., as a percentage of puppies produced). But the toll in number of puppies lost at birth or shortly thereafter is substantial. The mortality in Tonnessen's study represents deaths of 4,684 puppies over just the period from 2006 to 2007 in Sweden. That's a lot of puppies to lose, year after year after year in one country, but you have to appreciate that the toll worldwide would be in the many tens or hundreds of thousands.

With the cause of uterine inertia remaining undetermined, there are no recommended procedures for breeders to prevent the high rates of neonatal mortality. Without a cause for uterine inertia, it cannot be prevented, and the huge number of puppies that are perfectly formed but do not survive their first week in this world will continue to accrue.
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While observing the whelping of litters of more than 50 breeds of dogs over the last few years, I have inadvertently discovered that uterine inertia in dogs appears to be caused by light.

When the whelping room was kept dark, bitches were calmer and more relaxed, and puppies were expelled easily and without straining. Visible abdominal contractions were infrequent. The intervals between puppies were generally short, ranging from 10-30 minutes. When darkness was maintained through whelping of the entire litter, there were no stillborn puppies or pups born in distress. The puppies were vigorous as soon as they were released from the membranes and were able to find and attach to teats without assistance. Between puppies, the bitch cared for the puppies but was relaxed and without signs of stress.

If the bitch was exposed to any light during whelping, as for example by turning on a light or even a cell phone, the appearance of the bitch changed. She appeared less relaxed and abdominal contractions began. This usually lasted for about two hours after the light event and the whelping room was again completely dark. All of the stillborn puppies we observed were born after periods of exposure of the bitch to light with one exception, in which the last puppy in a litter of 15 was stillborn.

There is every reason to suspect that ambient light is the cause of uterine inertia during whelping in dogs. If this is true, the solution to high puppy mortality in dogs is management of light during the few hours when the bitch is whelping. ​My experiences controlling light during whelping indicate that this is the case.

It makes sense that the physiology of the dog is designed for whelping in the dark.

Wolves and free-living dogs whelp their puppies in underground dens, and the puppies remain in the den for several weeks. Our household pets seek out dark places as whelping nears, disappearing under the bed, in a closet, or behind a piece of furniture. We assume they are looking for a place that is protected, quiet, and cozy, and this might be true. But the key attraction for the dog might be darkness. 

Nevertheless, bitches whelping in the house are typically provided a box in a location convenient for monitoring, such as a bedroom, family room area, or even by a window. Because breeders generally supervise and assist with whelping, lighting is at least sufficient for the breeder to see even if it is dim.

The unintended consequence of the way we generally whelp puppies is that the difficulties encountered during labor that motivate close supervision by breeders are, in fact, caused by that very supervision, because it requires ambient light for the breeder to see. The best of intentions result in making whelping significantly more difficult.

​But we should be able to dramatically reduce mortality of newborn puppies. 

We need to give the bitch access to the conditions that her instincts tell her are best suited for whelping and raising her puppies, instead of what suits our convenience. The physiology of dogs and many other mammals is designed to give birth in the dark. We need to give her darkness.

This is routinely done by keepers of zoo animals, who carefully consider the biology and natural history of an animal in its natural environment in designing its habitat in captivity. Staff supervise by video and intervene if necessary, but, more often than not, birth proceeds without complication or intervention.

Dogs are quite good at reproducing themselves if left to their own devices. We should have fewer complications and much greater success with a simple strategy: just give her what she needs and get out of her way.
​

We need a new approach to whelping dogs that is better suited to their biology. I am calling it "dark whelping". 

Breeders are asking me questions about dark whelping:

• How dark does it have to be?
• Does it need to be dark only during labor, or before (or after) as well?
• Is turning a light on very quickly okay? 
• ​What about a really dim light?
• Is a red heat lamp ok to use?​

Unfortunately, the answer to these questions like these is usually "I don't know".

The dark whelpings I have done have been in absolute darkness (i.e., can't see your hand in front of your face), because this is a light level that can be replicated by every breeder (as opposed to various unknown levels of dimness). Under these conditions, with total darkness and no unplanned "light events", our puppy mortality has been zero.

Total darkness is difficult to do in the typical household. It takes planning and working out critical bits of the logistics ahead of time (e.g., how to retrieve the puppies for weighing without introducing light to the whelping room). But we have been doing it with success, and the extra trouble over a more convenient whelping box in the living room or bedroom is well worth the prevention of mortality.

I can't provide you with a protocol to set up dark whelping yourself. Every breeder's setup is different, and there will be different issues to resolve for the ideal setup for each litter. I can tell you that the process seems to be extremely sensitive to light, and getting it wrong often results in dead puppies.

However, if you would like to whelp a litter in the dark, you can contact me for assistance. I have experience with enough litters now to have worked out at least some of the problems you are likely to encounter.
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We have been whelping dogs for decades the same way, in a box in the house. We know nearly nothing about doing it in the dark beyond the fiddling I have done so far. For dark whelping, we will need research to nail down the necessary and sufficient conditions for success.

The sooner we can figure out how to do this right and provide breeders with a protocol they can follow, the sooner we can reduce the tragic loss of puppies that simply run out of oxygen before they make it out into the real world.

It won't take millions of dollars and many years to learn more about this. I just need breeders with upcoming litters and some financial support for my time to assist with logistics and guidance for breeders, and to record the outcome of a whelping event so I can prepare a protocol breeders can follow. There is lots of compelling research that will come out of this new information about whelping dogs, but for now my priority is to reduce puppy mortality as quickly as possible.

We can prevent puppy mortality from uterine inertia in your very next litter.

You can learn more about our project to prevent uterine inertia and reduce puppy mortality in our Facebook group, Uterine Inertia and Neonatal Morality in Dogs.

If you are interested in supporting the development of a protocol for dark whelping that breeders can use to reduce puppy mortality, please contact me. 

REFERENCES

Bergstrom A, et al. 2006. Primary uterine intertia in 27 bitches: aetiology and treatment. J Small Anim Pract 47: 456-460.

Cornelius AJ et al. 2019. Identifying risk factors for canine dystocia and stillbirths. Theriogenology 128: 201-206.

​Gill MA, 2001. Perinatal and late neonatal mortality in the dog. PhD Thesis, University of Sydney.

Olcese J, 2015. Using light to regulate uterine contractions. US Patent No US 8,992,589

Prashantkumar, KA and A Walikar. 2018. Evaluation of treatment protocols for complete primary uterine inertia in female dogs. Pharma Innov J 7:661-664.

Tonnessen R, et al. 2012. Canine perinatal mortality: a cohort study of 224 breeds. Theriogenology 77: 1788-1801.

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There is detailed information about this study (Gill 2001):

​What is causing such high rates of mortality in puppies?

Excluding the puppies with evident abnormality, the necropsy information for the puppies in Gill's (2001) study (see below) shows that the stillborn puppies suffered from in utero hypoxia - they ran out of oxygen before they were born. In fact, even the puppies that were born live and lived for days also often show evidence of hypoxia (inadequate oxygen) in utero (from Gill 2001). (See necropsy reports below)

Using data for the time of birth of each consecutive puppy, you can compute the "inter-pup interval" as an estimate of how long it takes each puppy to be born (assuming that the placenta was detached at the beginning of that period).

​This graph shows that a longer interval between puppies increases the risk of stillbirth. (The first point on the graph represents puppies with inter-pup intervals from 0 to 60 minutes; the marker is placed at 30 min.) 
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So, as the time between births increases, the proportion of stillborn puppies increases.

But why does birth of puppies take so long? 

The pace of labor is determined by the contractile behavior of the uterus. Prolonged labor is the result of "uterine inertia", which is a failure of the uterus to contract with sufficient strength and frequency to expel the puppy.

If we could prevent uterine inertia, we could potentially greatly reduce puppy mortality, both as stillbirths and for puppies that survive for days or even weeks but ultimately die.

When I ran into this issue of high puppy mortality, I was surprised that it had not been resolved long ago. After all, we can determine cause of death, and for most puppies it seems to be a matter of physiology (hypoxia), not a mysterious pathogen or anatomical abnormality. The high mortality of puppies has been well documented, but several studies that searched for a cause came up empty.

If puppies are suffocating in utero because of uterine inertia, then that's the problem we need to solve.

I found various suggestions of possible causes (e.g., overstretching of the uterine muscle, exhaustion of the uterus), but no explanation in the canine or veterinary literature.

However, I stumbled on what I think is the answer.

Here are some representative data for uterine contractions during labor in a human. Starting in a dark room, the frequency of contractions increases by the hour. If a light is turned on for an hour, the contraction rate drops dramatically to only 1/hr. When the light is turned off, contractions recover slowly.

​

But does this also happen in dogs? In fact, it looks like it does.

My colleagues and a group of cooperative breeders have found that bitches kept in a room with lights on typically produce a couple of puppies, but then there is often a prolonged interval before the next puppy appears. In the meantime, the bitch is typically restless and producing strong abdominal contractions. When puppies are produced, the intervals between them can be protracted - an hour or two, or sometimes many hours or even the next day.

But we have found that when the whelping box is in a dark room - a VERY dark room - the bitch is relaxed and calm, and the puppies are expelled quickly and easily, without straining and abdominal contractions. The pups are vigorous as soon as they emerge from the membranes, and the bitch tends to each without assistance.

Most notably, as long as the whelping room stays dark, there are no stillborns or puppies needing reviving. 

However, if a light are turned on, even very briefly, the strong abdominal contractions resume, but there are long intervals between puppies. Some of these puppies are born with fluid in the respiratory tract or need to be revived, and some can be stillborn.

If light is the key to reducing puppy mortality, it could have huge implications for canine husbandry. Not only would there be fewer losses to morbidity and mortality, there would also be fewer emergency c-sections to recover puppies trapped by unproductive labor, and less risk of losing a bitch because of a difficult labor.

The significance of this doesn't escape me. We will need to do some careful studies to verify the effects of light and darkness on whelping, and there is a long list of questions about effects on physiology and behavior that should be addressed. But as problems go, this one is potentially very easy to solve. And it will result in more puppies. That's definitely a win.

VIDEO: Bernese Mountain Dog, dark whelping. 

This is typical for bitches whelping in the dark. The bitch is relaxed and not straining. The puppy emerges quickly and mom takes caresof it to remove membranes and lick clean. (Watch carefully!)

​Pathology of Puppies That Survived < 48h

REFERENCES

Cornelius AJ et al, 2019. Identifying  risk factors for canine dystocia and stillbirths. Theriogenology 128: 201-206.

Gill, MA, 2001. Perinatal and late neonatal mortality in the dog. PhD Thesis, University of Sydney.
​
Tonnessen R et al, 2012. Canine perinatal mortality: a cohortt study of 224 breeds. Theriogenology 77: 1788-1801.

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The transition from fetus to neonate is physiologically strenuous for a puppy. Like an astronaut at the space station, working outside the station requires a transition from an environment with the adequate air pressure and oxygen for normal respiration, to one completely lacking these things. To survive a space walk outside the vehicle, the astronaut needs a suit that can be pressurized and provides oxygen. A failure of those systems to work properly is catastrophic.

A puppy faces similar challenges in its transition from fetus, where the placenta is its lifeline and supplies all of its needs, to a world in which its own physiological systems need to take over all of the processes necessary for life. The complexity of this transition is not physiologically trivial.

One of the techniques that has been used to remove the fluid from lungs of a puppy immediately after birth involves holding the puppy in the hand with arm extended and "swinging" the puppy, head down, in an arc. This will often successfully clear the fluid in the lungs so the pup can begin to breathe normally. I have seen many breeders do this, and there are videos and instructions online for those unfamiliar.

But swinging puppies to clear the airways is a really, really bad idea.

I have to confess that the first time I saw this done, it literally took my breath away (not a pun). Swinging might move the fluid out of the lungs, but it causes ALL of the fluids in the body to move towards the head of the puppy - blood, cerebrospinal fluids, stomach contents, and any other fluids in the body. This is NOT a good thing, and I will explain why.

Perhaps you have seen how astronauts are trained to tolerate the g-forces produced in space flight. They use a huge centrifuge with a capsule at the end of a long arm. The test subject is in the capsule, and as the centrifuge rotates, the g-force experienced by the human in the capsule increases; the faster the rotation, the greater the force.  

Take a few minutes to watch this video of the human centrifuge in action.

 

The expressions on that fellow's face tell you something about what you look like when the force of gravity is higher than your body is designed to tolerate. There is great pressure on the body, making it difficult to breathe, but, perhaps worse, the body fluid want to rush to the head. In an adult humans (and dogs), the physiological systems that control blood pressure kick in immediately to try to maintain normal fluid pressures in the organs and vessels.

Now think about the puppy with fluid in the lungs. (In a newborn, this will ilkely be amniotic fluid, but it can also be milk that is aspirated when nursing or being hand fed.) A newborn puppy is not a small version of an adult dog. Many of the organs are not mature at birth (e.g. eyes, kidneys), nor are the systems that control blood flow and regulation of blood pressure. In the newborn puppy, the circulatory system has a much lower pressure than in the adult dog, and the immature nervous system has very limited ability to control it (Grundy et al 2009).

Your body does a good job of regulating your blood pressure by changing the diameter of blood vessels (constrict or dilate) and increasing or decreasing the heart rate to keep blood pressure from going too high or too low. If you have ever stood up quickly and started to black out, this is your body momentarily failing to maintain the blood pressure in your head; in just a second or two, everything will return to normal as your body automatically adjusts blood pressure and heart rate to restore adequate oxygen delivery to your brain.

The systems to control blood pressure and tissue perfusion in the dog are essentially the same as your own, but they are not fully functional in the newborn puppy. A puppy is more like a premature human infant at birth, with organs systems and regulation not yet fully developed. Because of this, insults that would be handled easily by an adult dog can be much more challenging to the newborn puppy. Control of blood pressure is one of these.

This is a real problem if the puppy is swung in an arc to remove fluid from the lungs. Watch this fellow (a veterinarian, apparently) demonstrate.
​

 
Raise your hand if you gasped when you watched this. Or maybe you even stopped breathing. Think about that astronaut in the centrifuge. Try to imagine what would be happening inside the body of a tiny puppy.  That puppy is being swung HARD.

Yes, swinging might help remove fluid from the lungs of a newborn puppy. But it can also cause brain damage.

What happens to the brain of a puppy that has been swung to clear its airways?

The puppy might have no obvious signs of physical trauma; there are no surface lesions and few behavioral changes (after all, the puppies only have two activities, nurse and sleep). There can be seizures, which might be the only significant outward evidence of serious damage (Grundy et al 2009). However, examination of the brain tissues will reveal evidence of trauma manifested as subdural and intracerebral hemorrhage.

REFERENCES

Grundy SA, 2009. Clinically relevant physiology of the neonate. Vet. Clin. Small Anim. 36: 443-459.

Grundy et al 2009. Intracranial trauma in a dog due to being "swung" at birth. Topics in companion animal medicine 24: 100-103.
​

Back in the good old days, before the development of fancy scientific gadgets that can measure anything to the fifth decimal place, scientists did a lot of good science using very simple, familiar tools. A clever scientist could design experiments that provided information about the neurological basis of body temperature control in animals with nothing more than a heat lamp like the ones you use in your whelping box, and a fan and some water. Ingenuity, creativity, and keen powers of observation were traits of the most successful scientists, much as they still are today in a very different, highly technological context. ​I love reading these old studies. People these days tend to dismiss them because they seem primitive and simple-minded, but a lot of things we know now and take for granted were based on simple experiments cleverly done decades ago.

A good example of one of these was a study by Welker (1959) to learn how puppies are able to stay in contact with their most important heat sources, their mother and their littermates.

The reason you keep a heat source in your whelping box is because newborn puppies are altricial (not fully developed) at birth. Eyes and ears are closed, and they have only two useful senses (temperature and touch). A physiologist would describe a puppy as a "very simple system".

 One consequence of their relative prematurity at birth is that they are unable to generate metabolic heat to control their own body temperature. Although this ability develops over the first few weeks, at birth the puppy behaves pretty much like a water balloon, heating at about the same rate under a heat lamp, and cooling at about the same rate in the cold. Puppies are about 80% water, so the similarity is not surprising.

At the other extreme is heat, which physiological systems don't cope with very well. Puppies can suffer heat stroke just like an adult dog, causing tissue damage and ultimately shut-down of the physiological systems necessary for life. An adult dog has some ability to prevent heat stroke by increasing heat loss and limiting gain (e.g, panting). But the newborn puppy enters the world with few response options beyond trying to crawl to a suitable place. ​

Of course, the best way of prevent being exposed to a dangerously high or low temperature is for the puppy to avoid it in the first place. We would expect puppies to be pretty good at doing this (after all, the unsuccessful could die), but how?

Back in the 1950s, a scientist named Wexler at the University of Wisconsin did some simple but clever experiments to learn about how newborn puppies can avoid hot and cold to maintain a body temperature suited to their physiology. He used a 250 W infrared heat lamp to produce "warm" and "hot" conditions simply by holding it closer (about 1-2 ft away) or a bit farther away (about 4 ft)  from the puppy. For a cold condition, he moistened the skin of the puppy with water and used a fan to produce evaporative cooling. This was crude; the experimental conditions were subjective and qualitative, and probably not even repeatable. But it was a simple experiment that anyone could do (both then and now) if you had a heat lamp, a glass of water, a fan, and a puppy.

There were several questions Wexler wanted to address.

• Are puppies able to sense their own body temperate? If they can't do this, they can't take actions to regulate it. This would require the puppy to have a central heat sensor that communicates with the physiological systems involved in a response.

 

• Can puppies sense hot and cold objects in their environment? A puppy in a place that's too hot needs to know if it's moving towards a place that is coolerr, and likewise for its response to cold.

 

• Finally all of these must work together to produce the appropriate response by the puppy to get it from a dangerous place to a safe one.

Here's the setup. Wexler worked with 45 mongrel puppies that were 1-3 days old. He had a surface to put one or several puppies on (a table covered with a towel), and the tools for producing hot and cold temperatures (lamp, fan, and water).

The hot and cold conditions were applied until the puppy produced vocal and behavioral responses. The  effects of touching an object just using the fingers applied to various places on the body.

The Puppy Huddle
​
To address the first question about whether puppies can sense their own body temperature, Wexler put a group of 4 puppies on the table. Under cold conditions, the puppies gathered to form a huddle. After some time in the cold, the puppies became agitated and vocalized, but they only moved around within the pile and not away from it. If a heat lamp was directed at the pile of puppies, they became quiet within a few seconds. If the heat lamp was moved closer, vocalizations and movement began again in response to the higher temperature, and the puppies gradually moved apart from the huddle. When the puppies were all separated from each other to avoid the heat from the lamp, the lamp was turned off and activity and vocalizations stopped. The puppies would gradually cool until once again they got cold enough to stimulate  vocalization and movement. This phenomenon worked so well that the puppies could be induced to huddle and disperse over and over, simply by turning the heat lamp on and off. 

This demonstrated two things - first, that the puppies could sense their own body temperature and, second, that they could also moderate their response to body temperature with a skin sensor that could detect both pressure when in contact with littermates, and temperature; that is, whether an object was hot or cold.
​

The Single Puppy

​The behavior of individual puppies in response to heat or cold was even more interesting. 

A lone puppy in the cold sweeps its head from side to side, emitting a cry with each respiration, and occasionally moves forward a short distance. Similar side to side movements of the head occur under hot conditions, again with cries on respiration. While it might take 30 to 60 seconds with the heat lamp turned on to simulate the head movements and vocalizations, both stopped almost immediately when the lamp was turned off. If the lamp was turned on again, the response of the puppy was almost immediate, in contrast to the slower response with the first exposure to heat. This would require thermal sensors on the skin that stimulate a central receptor almost immediately. 

In the trials under hot conditions, the temperature of the fingers mattered. Touching a cool puppy's nose with a warm finger caused the puppy to move forward, while touching both cold and hot puppies with cold fingers stimulated withdrawal and avoidance behavior.

​This response of newborn puppies to touch was remarkably strong. A puppy could travel a distance of 50 yards in 15 minutes, stimulated simply by a bilateral touch on the nose. And perhaps even more remarkably, the puppies seemed to be as strong after this distance than when they started.

The Integrated Puppy

A newborn puppy might look helpless, with eyes closed and limited ability to move around, but it has remarkable sensory abilities that allow it to maintain some control of its body temperature and avoid extremes that would be dangerous or deadly. We know from simple studies like the one described here that puppies can sense their own body temperature, determine whether it is too high or too low, and take actions to move to a more thermally suitable place. The puppy can sense when it touches something and whether it is hot or cold, and it will move forward in response to a touch on the nose, something that might help it stay with its siblings or mother. 

What might look like random, pointless movements of puppies in your whelping box are actually evidence of the actions a newborn puppy takes to keep its body temperature in a suitable range for growth and physiological functions. Over the next days and weeks, the physiology of the puppy will mature and it will be able to generate and retain enough metabolic heat to maintain a stable body temperature, at which time it is able to become more independent.

​You can learn more about the science of dog breeding in my new online course, "The Science of Canine Husbandry", which is available through the Institute of Canine Biology.

REFERENCES
Welker, WI. 1959. Factors influencing aggregation of neonatal puppies. ​J. Comp. Physiol. Psych., 52(3), 376-380. https://doi.org/10.1037/h0047414

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​

I refer here to the essay by Geir Flyckt-Pedersen bemoaning the increasing burden of rules directed towards the breeding and showing of purebred dogs in the 7/30/2022 edition of ​Dog News.

Commercial livestock breeders enthusiastically adopted use of Wright's inbreeding coefficient to improve the efficiency and quality of their breeding programs. Indeed, this new "quantitative" tool to give insight into genetics revolutionized animal breeding in the 1940s, and this ability to determine relatedness of animals by estimating the inbreeding of their potential offspring is the guiding principle of genetic management in animal breeding still today. 

While animal breeding in general entered the age of modern genetics, dog breeding remained essentially unchanged. Even with the availability now of DNA testing, the dog fancy continues to use the breeding methods of yesterday. The commercial animal breeders of Wright's time would be able to explain to the dog fancier what to expect from breeding programs that ignored inbreeding - smaller litters, higher puppy mortality, shorter lifespan, less "vigor"; pretty much less of everything that defined the quality and value of the animal. 

So, Flyckt-Pedersen asks where did the "nonsense" of inbreeding coefficients come from? It comes from the basic principles of genetics that are the foundation of Wright's coefficient of inbreeding. Inbreeding coefficients most certainly did not suddenly appear; I would argue that it has been hiding in pain sight. It's been around for a century and continues to provide the foundation of successful breeding programs of all domestic animals (except dogs). In the last two decades, a far-sighted group of dog breeders with a scientific bent and interest in how things work began to understand the importance of population genetics in sustainable breeding of population sof animals. To this end, they homed right in on the consequences of inbreeding and how the inbreeding coefficient could be an essential tool for managing the health and quality of purebred dogs. While the circle of influence of these pioneers continues to spread, there are still many in the dog fancy that reject the notion that inbreeding can be detrimental and thus critically important for breeders to understand. These young breeders are hungry for information that will help them produce dogs of health and quality, and inevitably the older generation will pass on, and science instead of opinion and ideology will be the foundation of successful breeding of purebred dogs in the future.

As for restrictions on the number of times a sire can be used. Once again, these come from understanding the genetics of animal breeding. The reason for restrictions is very easy to understand the basic principles, and I refer you to this very basic blog post, The Pox of Popular Sires, that I wrote nearly a decade ago to guide you through understanding the consequences of popular sires.

For more on the coefficient of inbreeding, see "Is COI an essential tool or just a fad?, and many other blog posts on the ICB website.
​

REFERENCES
Wright, S. 1922. Coefficients of inbreeding and relationship. American Naturalist 56: 330-338. (PDF)

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

Why was estimating relatedness important? Back in the day, breeders understood the general effects of parental relatedness on quality of offspring. They knew that a bit of inbreeding increased the uniformity, predictability, and quality of many traits in offspring. But they also found that too much inbreeding had negative effects, a phenomenon called "inbreeding depression." Starting with a population of outbred animals, Wright summarized the dual consequences of inbreeding here (Wright 1922):

Wright's development of the coefficient of inbreeding revolutionized animal breeding because it provided a quantitative estimate of inbreeding based on an understanding of probability in inheritance of alleles. His expression of this has arguably been the most powerful tool in the box for breeders over the last century, and it remains just as important now as it was then because it is grounded on the fundamental processe of independent inheritance of alleles. In many populations of wild and captive animals (and plants, too!), the coefficient of inbreeding, and its related statistic, the kinship coefficient, remains the primary means of genetic management.

So why is it that I hear breeders declaring that "the inbreeding coefficient is "just a tool" or a "fad", or a crude, dusty relic of the olden days when breeders only used paper pedigrees for breeding? It is claimed to be "inaccurate", "pretty much worthless", and not useful now that we can estimate genomic inbreeding from DNA analysis. If this was true, why would today's foremost scientists in the fields of population genetics and animal breeding management still be using it? 

Well, I think a lot of breeders say these things because they heard somebody else say them. This is the "folklore" model of information development, where the loudest voices can produce "information" that is accepted by the masses because nobody does the fact check. People parrot these memes because it's what everybody else says, and they don't understand the biology enough to questions anything. The consequence is that you can't make the best breeding decisions working from bad information, and after all the work and expense that goes into breeding, nobody wants to do that! 

In truth, we will continue to use the coefficient of inbreeding as long as we continue to breed animals and plants, which will be as long as we inhabit this earth. Here are a few reasons why, and these are also the ways you should be using it now.

First, the inbreeding coefficient can be used to reconstruct the genetic history of a population of animals. Dr Pieter Oliehoek used it in his analysis of the population genetics of the Icelandic Sheepdog to document the loss of genetic diversity over time, as reflected in the increase in average level of inbreeding in the population.

Oliehoek also used a related statistic, the kinship coefficient, to reveal how breeding strategy in the population had changed over time. The kinship coefficient measures the degree of relatedness (in terms of genetic similarity) between two individuals. The kinship coefficient is also equal to the inbreeding coefficient of offspring produced by a pair of animals. In other words, the inbreeding coefficient of an animal is the kinship coefficient of its parents. When Oliehoek plotted both the inbreeding coefficient (black symbols and line on the graph below) and kinship coefficient (red symbols and line) on the same graph as probabilities (i.e., values between 0 and 1.0), he showed that in the early history of the breed, there was preferential avoidance inbreeding that is revealed because average inbreeding was less than average kinship in the population (the black line is lower than the red line); that is, breeders chose to pair individuals that were less closely related than average in the population. This was the case until the early 1980s, when these lines flipped, with the average inbreeding increasing faster than average kinship, reflecting a preference by breeders for closer inbreeding, even when pairs were available that would produce lower levels of inbreeding.

Oliehoek also used the kinship coefficient in a very clever way, to reveal the decline in the size of the gene pool over time. In the chart below, he used the relatedness of each animal in the population with every other animal in pairwise comparisons to compute "mean kinship" (Nmk), which is a measure of the size of the gene pool. This is expressed in terms of how many founder dogs would result in a gene pool of the same size, something called the "founder genome equivalents. This graph below shows that the population started with the equivalent of about 20 unrelated founder dogs in about 1955, but by 1975, only 15 years later, the size of the gene pool had dropped to the equivalent of only about three dogs, and it continued to decline in subsequent decades. By the end of the 1990s, breeders had the genetic diversity of only 2 dogs to work with. Again, this information is derived from calculation of the genetic relatedness among the dogs in the population from the kinship coefficients, which estimate the predicted COI that would result from a particular mating. 

The brown squares along the x-axis of the graph above represent the importation of new dogs into the population. Breeders assumed from scrutinizing pedigrees that these dogs were relatively unrelated to their breeding population and would therefore restore some lost genetic diversity and reduce the level of inbreeding. But Oliehoek once again used the kinship data to reveal that the population of the breed had clusters of related dogs, and that unfortunately, the imported animals were genetically part of the main cluster so did nothing to improve genetic diversity. The chart Oliehoek produced below showed where relatively less-related dogs could be found in other clusters, and it also showed that some of these other clusters were perilously small in size and at risk of extinction. Breeders could use this information to make better selections of dogs to import, and to also make sure that lines with small numbers of dogs were not accidently lost.

The Coefficient of Inbreeding has been around for a long time, and it is no less useful today than when it was first described by Wright a century ago. Genomics can now provide us with lots of information that was just a dream only a few years ago, and it's fair to say that we are in the midst of a new era of what can fairly be called "precision breeding" . But as long as breeders continue to use pedigrees when making their breeding plans, the inbreeding and kinship coefficients will continue to be used to estimate relatedness, predict litter inbreeding, and balance the benefits of prepotency and consistency with the risk of genetic disease and inbreeding depression. 

REFERENCES

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

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

The FCI, and most breeders, are missing the foremost reason why purebred dogs get bad press and have such a bad public perception. Inbreeding. To the lay person, it's incest. In fact, it should be to dog breeders as well. The average person knows that incest is bad, that it produces genetic problems, and that purebred dogs are inbred. They are not wrong. 
​

REFERENCES

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

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

It's hard to get anything out of a table of numbers, so I have produced a chart summarizing the data in their Table 2, plotting the percentage of dogs affected for each disorder, ranked by prevalence in Pugs.  (Note that they applied several statistical treatments to adjust for effects of age, weight, spay/neuter status, etc.)
​

It seems unlikely that these results reflect an unhealthy population of dogs produced by puppy mills and back yard breeders, vs the mainstream breeders in the dog fancy, because a number of these health issues result from traits stipulated in the breed standard (e.g., shortened muzzle, skin folds), but the data aren't there to support this assumption.
  

  

REFERENCES

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

REFERENCES

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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