The Institute of Canine Biology
  • HOME
  • Blog
  • Courses
    • COI BootCamp (FREE!)
    • Basic Population Genetics (FREE)
    • The Science of Canine Husbandry
    • Managing Genetics For the Future >
      • Syllabus - Managing Genetics for the Future
    • The Biology of Dogs (Open Reg )
    • DNA For Dog Breeders >
      • Syllabus - DNA for Dog Breeders
      • Open Reg - DNA For Dog Breeders
    • Understanding Hip & Elbow Dysplasia >
      • Open Reg - Understanding Hip & Elbow Dysplasia
    • Genetics of Behavior & Performance >
      • Syllabus - Genetics Behavior & Performance
      • Open Reg - Genetics of Behavior & Performance (Open Reg)
    • Strategies for Preservation Breeding >
      • Open Reg - Strategies for Preservation Breeding
    • Group Discounts
    • MORE FREE COURSES >
      • Quickie Genetics (Free!)
      • Heredity & Genetics (Free!)
      • Useful Genetics (Free!)
      • Basic Genetics Videos
  • Breed Preservation
    • Breed Status
    • Breeding for the future >
      • BFF Breed Groups
    • The "Elevator Pitch"
    • What's in the Gene Pool?
    • The Pox of Popular Sires
    • What population genetics can tell us about a breed
    • What population genetics can tell you...Tollers & Heelers
    • How to use kinship data
    • Using EBVs to breed better dogs >
      • How population size affects inbreeding
      • EBV Examples
    • How to read a dendrogram
    • Global Pedigree Project >
      • The Database
    • Finding the genes without DNA
    • How to read a heat map
  • Health Data
    • Bloat (Purdue Study)
    • Body Condition Score >
      • % Dysplastic vs BCS
    • Breed Comparions
    • Cancer
    • Cardiac
    • Cataracts
    • Caesareans
    • Deafness
    • Degenerative Myelopathy
    • Elbow Dysplasia
    • Epilepsy
    • Genetic Diversity
    • Genetic Diversity (MyDogDNA)
    • Hip Dysplasia >
      • Hip Dysplasia (Hou et al 2013)
    • Inbreeding Effects
    • Inbreeding (Gubbels)
    • Inbreeding (Dreger)
    • Lifespan
    • Litter size
    • Metabolic
    • mtDNA
    • Orthopedic
    • Mode of Inheritance
    • Patella Luxation
    • Thyroid
    • Portosystemic shunt
    • Purebred vs Mixed (UC Davis)
    • Purebred vs Mixed Breed (Bonnett)
    • Spay & Neuter Effects
    • Calboli et al 2008
    • Hodgman (1963)
    • Scott & Fuller (1965)
    • Stockard: Purebred crosses
    • Summers (2011)
  • Projects
    • How To Interpret Breed Analyses
    • Afghan Hound
    • More details about the Toller study
    • Belgian Tervuren >
      • Belgian Terv p2
      • Belgians- why population size matters
    • Bernese Mountain Dog
    • Boxer
    • Brussels Griffon
    • Bullmastiff
    • Canaan Dog >
      • Canaan analyses
    • Cesky Terrier >
      • Cesky genetic history
    • Chinook
    • Curly-coated Retriever
    • Doberman
    • Entelbucher Mountain Dog
    • Flatcoat Retriever
    • French Bulldog
    • German Shorthair
    • Golden Retriever >
      • Golden Retriever Pedigree Charts
    • Irish Water Spaniel >
      • IWS (6 Nov 17)
    • Labrador Retriever
    • Manchester Terrier
    • Mongolian Bankhar >
      • Research Updates
      • Bankhar 1
    • Norwegian Lundehund
    • Plummer Terrier
    • Otterhound
    • Portuguese Water Dog >
      • Portuguese Water Dog (pt 2)
    • Ridgeback
    • Schipperke
    • Standard Poodle >
      • The Problem With Poodles
      • 3poodle pedigree charts
      • 3Poodle Wycliff dogs
      • Poodle Genetics
    • Tibetan Spaniel
    • Tibetan Mastiff
    • West Highland White Terrier
    • Whippet
    • Wirehaired Pointing Griffons
    • UK KC Graphs >
      • UK KC Breed Status
      • UK Groups
      • KC Gundogs
      • KC Hounds
      • KC Terriers >
        • Terriers (select breeds)
      • KC Pastoral
      • KC Toys
      • KC Working
      • KC Utility
      • Australian KC
    • Breed outcrossing programs
  • Resources
    • Genetics Databases
    • Stud Books >
      • American Kennel Club stud books
      • Field Dog stud books
      • The Kennel Club (UK)
    • Learn
    • Videos about dog genetics
    • The Amazing Things Dogs Do! (videos) >
      • Livestock Management
      • Livestock guarding
      • Transportation, exploration, racing
      • Conservation & wildlife management
      • Detection Dogs
      • Medicine & Research
      • Entertainment
      • AKC/CHF Podcasts
    • Read & Watch
    • Bookshelf
  • Preventing Uterine Inertia

Are breeding restrictions putting your breed at risk?

1/6/2019

 
By Carol Beuchat PhD

There might be thousands of dogs in your breed, but the ones that are bred and pass their genes to the next generation are the only ones that really count in terms of genetics.

​In most breeds, only 20-30% of the dogs produced are used for breeding. The rest go to pet homes, usually with a contract that stipulates that the dog cannot be bred or offspring cannot be registered. These dogs join the ranks of the spayed and neutered. This means that the number of dogs producing offspring in a breed is much less than the census number. This has significant consequences for the genetics of the breed. ​

Picture
Let's Simulate!
There are some fun tools we can use to explore the effects on genetics of changes to some of the properties of a population. This is one that we use in my population genetics courses to help students understand how genetics can be affected by changes in various properties of a population such as size or addition of new individuals.

One of these is an online population simulator called Red Lynx. It's easy to use, and if you have access to the internet you can take it for a test drive.

Go the the Red Lynx website at ​https://cartwrig.ht/apps/redlynx/. 
On the landing page, click on the button to start the Red Lynx simulator.
Picture

This will take you to the simulator and you should see the screen below.

Red Lynx simulates the "behavior" of a single allele, "A1", in populations with various properties. There are two alleles at every locus, so actually A1 has a pair (lets call it A2). But we only need to simulate one allele, because if the frequency of allele A1 in a population is going up, the frequency of A2 must go down. If we model the behavior of A1, we know that A2 will be responding as a mirror image. So, we will run our simulations using only a single allele at a locus.

On the simulation page, you will see a graph, and below that a series of parameters that you can change using some simple sliders. We are only going to play with the first three: number of generations, population size, and initial allele frequency (green arrows). You can change these either by using the slider or just type the number you want in the box. You can ignore the rest of the sliders on the page.
Picture

Okay, let's see what this does. Let's start with the default values when you first go to the page, which are 2000 generations, population size of 800, and initial frequency of A1 as 50% (so we know that the frequency of A2 will also be  50%). Click on "Run Simulation" (red arrow). A line will appear on the graph.
​

Picture

​This line is the predicted behavior of the allele A1 in this population over time, assuming a 50/50 chance of inheriting the allele at each generation in a population under "ideal" conditions - no selection, no migration of A1 alleles in or out of the population, and no mutation. You can see that the initial frequency is 50%, and from there it change in frequency in the population with each generation.

Now, without clearing the graph, do a few more simulations. Each of these lines will be different because the role of chance in inheritance at each generation. If you do enough of these, you might see one of the lines go either all the way to 0% and flat-line (red arrow), or to 100% and stay there (green line). In the first case, all copies of the red allele have been lost from the population; for the green arrow, the alternative allele (A2) has been lost completely, leaving only A1, a situation we call "fixed" for that allele.
​
Picture

So what?

I hear you say "That's cool, but so what?".

Let's say the A1 allele was for something like the ability to smell a particular scent. If this isn't something you would be selecting for, this simulation suggests that there is a chance it could be lost from the population just by chance, a phenomenon called "genetic drift". Maybe this scent wasn't important to you, but if it was to the dog (e.g., a pheromone), it would have consequences that might affect some aspect of the physiology or behavior of the dog. Perhaps it is an allele that prevents fearfulness; losing it from the breed would definitely have consequences for the welfare of the dog. Or maybe it is an allele at a locus that is most beneficial when heterozygous - that is, the genotype A1A2 is more beneficial to the dog than either A1A1 or A2A2, something called "over-dominance". If one of the alleles is inadvertently lost from the population, all individuals will be homozygous for the other allele, and beneficial effects of heterozygosity will be unavailable.
So now let's do the fun stuff.

Let's make the number of generations in the simulation 100 so it will be more relevant to dog breeding. Change the population size to 50, and leave the allele frequency at 50%. Use the button to clear the graph, and run some simulations. 

You should find that the frequency of A1 goes to one extreme or the other (0% or 100%) in many of these simulations. 

Now run some simulations with different population sizes, perhaps 100 and 25. How does this affect the graph?

This simulator makes it easy to explore the effect of population size on the behavior of alleles in the population that you might not be paying any attention to. Clearly, the genetic stability of a population is sensitive to the number of individuals.

Why does this matter to your breed?

How big is your breed? What fraction of the puppies produced are used for breeding? Remember, only reproducing animals count when we're considering genetics. What are the effects of breeding contracts or spay/neuter policies on the population genetics of your breed? How stable is it genetically to the chance loss of alleles by genetic drift?

These changes in allele frequency occur in all populations. If a population is divided into closed subpopulations, the same phenomenon will occur in each of them. This will cause them to drift apart genetically over time. Breeders can take advantage of the genetic differences in these subpopulations to use them as outcrosses that can restore alleles that have been lost in another subpopulation. You can simulate this using the slider for "migration". If breeders can work together to monitor the genetic status of these subpopulations in a breed, they can reduce the loss of genetic diversity, slow the increase in inbreeding, and benefit from the hybrid vigor produced by an outcross.

​Is the population of your breed stable, or is it one of the many with registrations dropping off and fewer active breeders than there used to be? The simplest thing you can do to reduce the chance of losing important genetic diversity from your breed is to use more of the dogs produced in the breeding program. If the usual fraction is 20%, increase it to 40% or more. Don't send so many puppies off with contracts that prohibit breeding, or breed once before spaying or neutering. How much of a difference will it make? You can check it out using the Red Lynx simulator. Just remember that the simulator assumes a population with no selection, no migration, and no mutation (unless you stipulate conditions for these using the sliders). Certainly a purebred population will be under selection for the traits for type, but you can assume there is no selection for the "neutral" alleles that have no effect on type.
This simulator can also have a very practical use. Let's say your breed is discussing separating various colors in the breed into separate populations that would not interbreed. Or perhaps it is different sizes, or some feature of phenotype. If the groups are prevented from interbreeding, what will the consequences be for the genetic stability of the resulting smaller populations? There are many examples of breeds being split in the past - Norwich and Norfolk were separated based on ears, Toy and Standard Manchester were separated by size, the Belgian Shepherds are separated in the US based on color (but not in Europe), and perhaps you know of others. Splitting a breed WILL have consequences to the genetics of the separate populations, as you can see here effects of genetic drift on allele frequency. There will also be changes in other genetic properties of the populations such as the rate of inbreeding, and breeders should carefully consider these before deciding to make any changes in the breed.

You can learn more cool stuff about population genetics in ICB's online courses!
​Check out what we offer

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

Comments are closed.

    Archives

    January 2025
    November 2022
    July 2022
    May 2022
    April 2022
    March 2022
    February 2022
    November 2021
    October 2021
    December 2020
    January 2020
    August 2019
    July 2019
    June 2019
    May 2019
    April 2019
    March 2019
    February 2019
    January 2019
    December 2018
    November 2018
    September 2018
    August 2018
    July 2018
    June 2018
    May 2018
    October 2017
    August 2017
    May 2017
    April 2017
    March 2017
    February 2017
    January 2017
    December 2016
    November 2016
    September 2016
    August 2016
    July 2016
    June 2016
    April 2016
    March 2016
    February 2016
    January 2016
    December 2015
    November 2015
    October 2015
    September 2015
    August 2015
    July 2015
    June 2015
    May 2015
    April 2015
    March 2015
    January 2015
    December 2014
    November 2014
    October 2014
    September 2014
    August 2014
    July 2014
    June 2014
    May 2014
    February 2014
    December 2013
    October 2013
    September 2013
    July 2013
    March 2013
    July 2012
    April 2012

    Categories

    All
    Behavior
    Border-collie
    Herding

Blog

News


About Us

Contact Us








Copyright © 2012-2017 Institute of Canine Biology
Picture
Picture