By Carol Beuchat PhD
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.
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!
Above, all, have fun!
Genetic Management: Basic Strategy
Managing Genetics for the Future (Module 13, unit 1)
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.
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?
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.
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.
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.
To learn more about the genetics of dogs, check out
ICB's online courses
***************************************
Visit our Facebook Groups
ICB Institute of Canine Biology
...the latest canine news and research
ICB Breeding for the Future
...the science of animal breeding
ICB's online courses
***************************************
Visit our Facebook Groups
ICB Institute of Canine Biology
...the latest canine news and research
ICB Breeding for the Future
...the science of animal breeding
