# Putting “population genetics” to practice – a better way to think about breeding?



## LifeofRiley (Oct 20, 2011)

Up until a couple of years ago, I gave little to no thought to the world of breeding or purebred dogs (beyond the obvious problems)... it just wasn’t part of my dog world. Then, I fostered and adopted a GSD. My dog piqued my curiosity. He led me to want to better understand breed history and breed health. 

Somewhere along my learning curve, I discovered that the notion of a “purebred” dog is a relatively new cultural construct. Furthermore, I learned that this seemingly innocent cultural construct profoundly changed how breeders determined the breed-worthiness of any individual dog. 

In recent years, it seems there is a general consensus that those changes have had a detrimental impact on the overall health and stability of many breeds. 

My most recent readings have been focused on trying to understand what the breed fancy world sees as answers to these problems. 


On that note, I found some of Jeffrey Bragg’s thoughts on this topic to be interesting. *Here is the link to an article titled “Population Genetics in Practice: Principles for the breeder”* - Population Genetics in Practice

To me, many of these principles make a lot of sense. It would take up too much space on here to include all the details, but here is a bullet-point list of the principles:

Maintain balance of sires and dams
Eschew incestuous matings (linebreeding)
Understand and monitor Coefficient of Inbreeding (COI)
Pay attention to the trend in COI
Calculate number of unique ancestors
Know the genetic load, but don’t obsess about it
Use pedigree analysis
Conserve sire and dam-line diversity
Practice assortative mating
Maintain high generation time
Avoid repeat matings
Ensure sibling contribution
Monitor fitness indicators
Attempt founder balancing
Consider outcross matings
Monitor population growth
Seek balanced traits
Avoid unfit breeding stock
Avoid reproductive technology
Restrict artificial selection

Some key quotes:
“Restriction of the use of artificial selection may really be the most important principle of all, and the most difficult for the vast majority to accept. Breeders really should avoid all extremes of artificial selection!... The hard truth is that breeders’ selection itself is just as great a culprit, if not worse. Inbreeding and selection combine in a cyclical fashion in the dog world, to cause the systematic depletion ("depauperisation" to the geneticist) of purebred genomes. From the professional geneticist's standpoint, present-day purebred dog breeds are virtually all depauperate to a significant degree, therefore lowered in fitness, vulnerable to genetic disease and inbreeding depression. This situation is due to excessive artificial selection more than any other single factor.”

"...People's constant obsession with having the "best" dog and with "breeding only the best to the best," whether in dog-show terms, in dogsled racing, or whatever, creates a situation in which the best is definitely the enemy of the good.”

“Now that canine diversity has been stripped to the point that homozygous recessive "defect" genes are everywhere apparent, the dog fancy proposes to remedy the situation by embarking upon a new level of elevated selection, armed with DNA marker testing to enable the wholesale "elimination" of "defective" genes. This new wave of super-selection on top of the already extant depauperisation may well become the killer wave that will sink the ship of purebred dogdom, AKC, CKC, and The Kennel Club with it.”

*Another interesting read on this topic by John Armstrong:*
Population Genetics

Excerpt:
"In my view, the best strategy for dog breeders is carefully planned assortative mating combined with an attempt to minimize or at least reduce the inbreeding coefficient. In practice, if I am asked for an opinion on a suitable mate for a Standard Poodle, I suggest that the breeder assemble a list of dogs he/she would consider breeding to, based on conformation, temperament and whatever other criteria are deemed relevant, and I will tell them the inbreeding coefficient for each potential litter and also about the prominent ancestors in the pedigree. My personal criterion is a 10-generation COI under 10%, but I might pick one close to that, or even a bit over, if I liked the other qualities."

"...The COI has predictive value. I can tell you that an SP inbred to only 5% will, on average, live about 3 years longer than one bred to 35%, and I can tell you that a 10% increase will likely reduce litter size by about 7%.... I understand why breeders inbreed (or linebreed), but I don't agree that it is necessary to produce good dogs (see Inbreeding and Diversity). As to the claim that it can be used to uncover problems in the line, I agree, but I can also give you case histories where the breeder has proceeded to ignore a hereditary problem uncovered this way, and as a result spread it through the breed.
Neither population genetics nor modern DNA technology is going to provide magical solutions to all our problems. However, used together, they may take us through the 21st Century. Continued reliance on the models put forward in the early days of genetics almost certainly will not."

*So, I am interested in hearing everyone’s thoughts!!! *

I do have some particular question for the breeders on this forum:

Are the authors out in left field with these thoughts, or do others share his position?
Are breeders using the tools he referenced – or newer versions of them? How widespread is that use?
What role, if any, do you think these principles (and tools) could play in establishing new breeding/registration requirements (at the club and registry level)?

_Btw, I imagine some of the breeders on here have heard of the authors because at least one of them does not seem to be shy in stating is POV on a lot of different topics that pertain to the current state of breeds, breed clubs, registries, legislation.... you name it! I, personally, don’t agree with his views on legislation (or oversight of any kind), but I found a lot of his stuff to be an interesting read nonetheless : ) 
_


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## Merciel (Apr 25, 2013)

I would guess this topic is probably old hat to any serious breeder, but it's new to me as well, and something that I've been thinking about recently, so I'm glad you opened up a chance to discuss it. 

I wonder if there is anything that those of us who aren't breeders, and have no plans to become breeders, can do to help. What is the best course for people in that position? Take a dog from less-usual lines and title/test it for possible use in other breeders' programs? Something else? _Is_ there anything we can do?


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## hunterisgreat (Jan 30, 2011)

Merciel said:


> I would guess this topic is probably old hat to any serious breeder, but it's new to me as well, and something that I've been thinking about recently, so I'm glad you opened up a chance to discuss it.
> 
> I wonder if there is anything that those of us who aren't breeders, and have no plans to become breeders, can do to help. What is the best course for people in that position? Take a dog from less-usual lines and title/test it for possible use in other breeders' programs? Something else? _Is_ there anything we can do?


I only have a novice understanding of breeding & pedigrees... but:
It certainly helps to have a diverse set of proven dogs to chose from, however part of the problem, as stated above, is inbreeding to "fix" traits... if I consider breeding my dog to your very different (genetically) dog, I can expect the litter to be less consistent, and many of the traits that were "fixed" to the bloodline through inbreeding/linebreeding to be "unfixed" by the fresh genes.


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## Merciel (Apr 25, 2013)

Yeah, and that's a concern for me as a puppy buyer too, since obviously I want to stack the deck in terms of getting the biddability, drives, and athleticism needed to excel in my sports of choice. And that means I can't get too wacky in choosing "diverse" bloodlines just for the sake of diversity, especially since I don't know nearly enough to take a gamble on anything that isn't at least _mostly_ a sure thing.

I'd like to think there's a happy medium somewhere, but I'm so ignorant on this topic that I don't know where to find it or even really where to start looking.


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## Chris Wild (Dec 14, 2001)

Merciel is right that this is sort of "old hat" to a serious breeder in the sense that most of what is being discussed in the article are major considerations and talking points for breeders and have been for a long time. Though they do tend to generally be discussed within breeding circles, so most people probably don't know about this part of the science of breeding that breeders use. There are many email lists and other areas where breeders around the country/world discuss these things. One in particular that I and several other forum members belong to that puts a lot of emphasis on the tail male and female lines and their unique genetic contributions, one of the probably lesser known aspects of pedigree analysis that the article mentions.

The trick of course is finding balance between the things discussed in the article and other factors that are major concerns in a breeding program. 

One, that others have mentioned, is balancing maintaining good dogs that are good representatives of the breed, and some consistency within the bloodlines and breeding program, while maintaining some genetic diversity and reducing the risk of combining recessives to cause problems. Nothing but outcrossing, even when breeding "like to like" within the same breed, produces results that can be all over the place in terms of both physical appearance and temperament. Linebreeding and backmassing concentrates genes and brings more consistency, but of course it concentrates the bad as well as the good which is why it's so important for a breeder to have a thorough, in depth understanding of the lines being doubled up on and the traits that they bring. Most breeders use a combination of the two, alternating between inbreeding and outcrossing in a thoughtful manner as the generations progress. Of course, the more a breeder has a single, narrow focus of their program, such as winning in the conformation ring or winning on the SchH field or producing the ultimate dog for X endeavor, the more inclined they are to fall prey to the popular sires syndrome and stick with a relatively narrow set of genetic combinations that are time proven to be successful.

The phrase about understanding the genetic load, but not obsessing over it, is one that often puts breeders at odds with pretty much everyone else including customers and those who are trying to find a way to pigeon hole a breeder into a "good" or "bad" category. This is becoming more prevalent, and a far greater concern amongst breeders, with the new genetic tests that are becoming available. The DM test is a prime example. This is something that many are obsessing about in recent years and now there are many breeders, buyers, and armchair critics who will say that anyone who would fail to test their breeding stock and breed anything less than a normal to a normal must not care about health and is a bad breeder. Nevermind that there are serious doubts on whether the test is even accurate for GSDs, the bigger problem is that restricting the genepool to just those dogs who are normal for that one single gene is bad for the overall genetic health of the breed. Sure, it might eliminate DM, but at the cost of severely limiting the genetic diversity within a breed that is already somewhat bottlenecked in many lines, and there is also the concern that has been proven time and again that focusing breeding on eliminating one trait is going to concentrate others which will likely lead to a huge increase in other genetic health and temperament problems.

Those are the main thoughts off the top of my head. May be more later. Right now I need to finish up some work and then head home to play with dogs.


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## LifeofRiley (Oct 20, 2011)

Chris Wild said:


> The phrase about understanding the genetic load, but not obsessing over it, is one that often puts breeders at odds with pretty much everyone else including customers and those who are trying to find a way to pigeon hole a breeder into a "good" or "bad" category. This is becoming more prevalent, and a far greater concern amongst breeders, with the new genetic tests that are becoming available. The DM test is a prime example. This is something that many are obsessing about in recent years and now there are many breeders, buyers, and armchair critics who will say that anyone who would fail to test their breeding stock and breed anything less than a normal to a normal must not care about health and is a bad breeder. Nevermind that there are serious doubts on whether the test is even accurate for GSDs, *the bigger problem is that restricting the genepool to just those dogs who are normal for that one single gene is bad for the genetic health of the breed.* Sure, it might eliminate DM, but at the cost of severely limiting the genetic diversity within a breed that is already somewhat bottlenecked in many lines, but breeding that trait out is going to concentrate others which will likely lead to a huge increase in other genetic health and temperament problems.
> 
> Those are the main thoughts off the top of my head. May be more later. Right now I need to finish up some work and then head home to play with dogs.


Yes, the "genetic load" part is something I found very interesting too! I hope you do come back and comment further on the topic : )


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## hunterisgreat (Jan 30, 2011)

Chris Wild said:


> Merciel is right that this is sort of "old hat" to a serious breeder in the sense that most of what is being discussed in the article are major considerations and talking points for breeders and have been for a long time. Though they do tend to generally be discussed within breeding circles, so most people probably don't know about this part of the science of breeding that breeders use. There are many email lists and other areas where breeders around the country/world discuss these things. One in particular that I and several other forum members belong to that puts a lot of emphasis on the tail male and female lines and their unique genetic contributions, one of the probably lesser known aspects of pedigree analysis that the article mentions.
> 
> The trick of course is finding balance between the things discussed in the article and other factors that are major concerns in a breeding program.
> 
> ...


Yeah I think people fail to realize that there are likely many, many as of yet unidentified and unseen genetic issues that will begin rearing their head when the gene pool is sufficiently restricted for that gene to allow it's expression.


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## Chris Wild (Dec 14, 2001)

It doesn't even have to be unknown traits, though there probably are some.
The Seeing Eye focused great effort for many years on eliminating HD in their breeding program. And they pretty much succeeded. Only to find that they were then pumping out MegaE pups left and right, in numbers that far exceeded the norm for the breed.


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## Freestep (May 1, 2011)

LifeofRiley said:


> "...People's constant obsession with having the "best" dog and with "breeding only the best to the best," whether in dog-show terms, in dogsled racing, or whatever, creates a situation in which the best is definitely the enemy of the good.”


I agree. I think of Stephanitz saying (paraphrased) "The GSD should be best at nothing, and second-best at everything."

I try not to use the terms "best" and "bettering the breed" after it was pointed out to me that one person's idea of "best" and another's are going to differ, and that some peoples' idea of "best" means a profound detriment (think extreme angulation, roach backs, hyperactivity, etc.). What I was meaning by "bettering the breed" was to bring it closer to the written standard, but it's been interpreted as "bringing out the most extreme".

It's always a good idea when obsessing over pedigrees for specific traits, to back up and look at the big picture. Since I'm not a breeder, I haven't had to deal with these kinds of decisions, but I love to listen to breeders talk about why they make the choices they do.


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## LifeofRiley (Oct 20, 2011)

So, do breeders on here factor in COI in making breeding decisions? Or, is this just a pipe dream of the authors I cited?

I ask because I have never heard that particular acronym mentioned on this board. Of course, I am relatively new to this board so maybe it has already been discussed ad infinitum.


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## Merciel (Apr 25, 2013)

It's been discussed a couple of times on the board (and there are some interesting article links in those older threads), but I didn't know that until today when I did a search after this thread came up.


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## LifeofRiley (Oct 20, 2011)

Hi Merciel,

Thanks for the response! Can you point me in the direction of those threads, or post them on this thread? I have no clue how to post threads in an active thread... on top of that, I have found that doing searches on archives here to be a nightmare! Maybe that just shows my own age more than anything else :laugh:


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## Merciel (Apr 25, 2013)

Sure, no problem. 

http://www.germanshepherds.com/forum/current-dog-affairs/213362-top-world-dogs-their-coi.html

http://www.germanshepherds.com/forum/breeding-general/261529-coefficient-inbreeding.html

just to get started. I'm still following all the links so I haven't gotten past those two threads yet.


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## Merciel (Apr 25, 2013)

Aw man, I hope I didn't kill this thread. I really do think it's an interesting topic that I would like to learn more about.

When I was looking at those World Dogs COI links (The 2012 Dog World Top Stud Dogs ? Hooray For Inbreeding! | The Doggie Stylish Blog for ease of reference), it seemed like GSDs were doing okay as a breed. The breed average COI was listed as 3.4, and the site says that that the FCI recommends 6.0 or lower (the site itself seems to suggest that you should really be aiming for 3.0 or lower, though).

It's hard for me to tease out whether that breed average is representative of where the various lines stand, though. There are some big divisions in this breed, and while there's probably very little pedigree overlap between an American showline and a working-line dog, each of those subtypes might have a much higher COI within the type. COI isn't discussed quite as frequently as "linebreeding" or "backmassing" on this board, but they do seem to be related topics. So... how big a concern _is_ this in GSDs, practically speaking? I can't tell.

(For a minute I wondered whether the number might be artificially lowered by the number of basically random-bred pet dogs who are registered with the kennel club just so they can "have papers," but I don't think this is a factor because Labradors and Golden Retrievers both have substantially higher breed-average COIs and they're at least equally popular as pet dogs, if not more so. So based on that I am speculating that the pet dog population does not have a significant impact on how the COI numbers are calculated -- because unless the puppy mill problem is WAY bigger than I had assumed, I don't think most BYB dogs are significantly inbred. They may have other issues, but I would expect/hope they at least don't have that one.)


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## LifeofRiley (Oct 20, 2011)

Merciel said:


> Aw man, I hope I didn't kill this thread. I really do think it's an interesting topic that I would like to learn more about.


I don't think it was you. This thread just does not seem to have garnered much interest. It happens.

Regarding some of the questions you have about the genetic health of different populations of GSDs, I am really curious about that too! I wonder if it is just an unknown at this point. 

It seems that "population genetics" and "COI" is much more discussed (outside of breeding circles) in other parts of the world. Most of the articles and websites talking about this are from the other countries, particularly the UK. It seems, to my novice eye, that Pedigree Dogs Exposed really changed the conversation over there.


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## LifeofRiley (Oct 20, 2011)

Now, this may make for an interesting read once the first issue is released this fall. 

_"Canine Genetics and Epidemiology"_ is a peer-reviewed, open access, online journal publishing original research and review articles relating to all aspects of canine genetics and epidemiology.


Here is a link that talks more about it:
Pedigree Dogs Exposed - The Blog: New kid on the blog...

The discussion by commenters is a little all over the place (not unlike what happens here sometimes ) but there are some good nuggets in there too.


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## Catu (Sep 6, 2007)

Inbreeding is a concept usually talked about in this forum. OIC is only the number associated to it, but not something not discussed here not in other breeders sites. I use working-dog.eu to review pedigrees because I think its more accurate than the PDB, where anyone can do changes, and at least in that site you can get the IC and ALC of every breeding.

BTW, thanks for the link and the tip of the Journal, I'll review them now.


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## marbury (Apr 3, 2012)

I know COI is a big deal with standard poodles, or at least they talk about it a LOT in their forums when they're discussing breeding.

I think that it's similar to PennHIP in that it's a great plan with great opportunity to give breeders another tool to use in their selection of stock, but it has to have a larger subscriber base to be truly effective. So, so many "AKC breedings" take place without any knowledge of ancestry at all. Sometimes six generations are all dogs like "Joan" and "Sugar Loaf" with no kennel name or anything. If we had a better way to trace ALL the AKC breedings on record (not just the Pedigree Database, which is woefully shallow on ASLs and happily shallow on BYBs) I think the COI could make a larger impact in our breed.

But then again I have an exceptionally limited understanding of COI to begin with, so take that worth it's weight.


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## LifeofRiley (Oct 20, 2011)

Catu said:


> BTW, thanks for the link and the tip of the Journal, I'll review them now.


Hi Catu, the first issue of the Journal will not be published until this fall. It is currently reviewing submissions. The link is really just one that discusses the goal of the Journal.


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## Catu (Sep 6, 2007)

LifeofRiley said:


> Hi Catu, the first issue of the Journal will not be published until this fall. It is currently reviewing submissions. The link is really just one that discusses the goal of the Journal.


I really liked the article, so much that I'm now translating in to Spanish to share it on my dog community. I did notice about the Journal, but thanks anyway, I saved it on my Bookmarks


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## LifeofRiley (Oct 20, 2011)

Catu said:


> I really liked the article, so much that I'm now translating in to Spanish to share it on my dog community. *I did notice about the Journal, but thanks anyway, I saved it on my Bookmarks*


Re: the bolded part - okay, I wasn't sure so I didn't want you to be disappointed : ). The article you are translating, is it from the first posts on this thread or the latest one about the Journal itself? Just curious.


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## LifeofRiley (Oct 20, 2011)

Hi Catu, the more I think about the above question I asked you, the more it seems obvious that you were referring to the initial link. I think it is great that you are translating that. I, too, found it to be very interesting.

Sorry for the confusion, I think the mimosa at brunch went to my head... lol!


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## Catu (Sep 6, 2007)

LifeofRiley said:


> Hi Catu, the more I think about the above question I asked you, the more it seems obvious that you were referring to the initial link. I think it is great that you are translating that. I, too, found it to be very interesting.
> 
> Sorry for the confusion, I think the mimosa at brunch went to my head... lol!


:thumbup: Saturdays are to be enjoyed.


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## Catu (Sep 6, 2007)

LifeofRiley said:


> Hi Catu, the more I think about the above question I asked you, the more it seems obvious that you were referring to the initial link. I think it is great that you are translating that. I, too, found it to be very interesting.


And now I also got written permission from the author to share my translated version


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## LifeofRiley (Oct 20, 2011)

Catu said:


> And now I also got written permission from the author to share my translated version


I think it is great that you reached out to the author! Keep us posted on how people respond to the article in your country!


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