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Breeding - The Big Picture

Thank you for this post. I have culled in my litters, often if you watch the dam she will also que to any unfit pups as well, be it out right rejection of one or two pups while fully excepting all others, or just a little less attention on her part to the pup in question. If you wait and watch those pups you will see that they are weaker, or in one case of mine actually had a defect in her digestion, that we found through an exam with my vet. Many people would not want to know about a culls in a litter, but the dam and the remaining pups are always healthier for it. And I feel ok knowing that no future families will have the heartache of dealing with health issues in the future. And the dog will not be in distress or pain. Thank you again for this post, and yes culling does not always have to mean actually ending the pups life, spay, neuter and many other methods are helpful. It's case by case every one is different.
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  • Breeding - the big picture by Astibus. Dan wrote this article on his http://sharplaninec.com website and I thought it would stimulate some good discussions here. Article follows:

    BREEDING - The Big Picture!

    Keywords: Population Genetics, Culling, Linebreeding

    Many articles have been written about dog breeding, with the better ones usually covering some aspect of canine genetics as well. However, even those latter manuscripts merely revolve around Mendelian genetics. While this is undoubtedly valuable for the understanding of inheritance when breeding individual dogs, I have seldom encountered resources, where the authors tried to put dog breeding into a broader context.

    The question is, would our perception increase, if we took the focus away from single dogs or even individual breeding programs and started looking at breeds in their entirety? Is there any tangible benefit to interpreting our breeding efforts in the light of the impact on the complete breed?

    Whenever we consider a dog breed as a whole, the term Population Genetics should come to mind right away. But what exactly is Population Genetics? Well, it essentially describes a discipline within genetics, where quantitative tools are applied to understand global genetic drift, gene migrations, allele frequencies of certain desired or undesired traits etc. This outlook - as I will try to illustrate here - has far reaching and I believe fascinating implications.

    Let us dive into this matter with a little thought experiment at the beginning.

    Suppose you decided to recreate a breed of antiquity, which to all accounts has been extinct for centuries. To your own amazement, you were able to identify say 4 unrelated males that express this presumably ancient phenotype and another 7 females, all hidden away in various remote areas of the world. This basically becomes your "foundation" or in genetics terms comprises the gene pool of your new breed.

    So far so good. But once you start breeding them methodically, you soon realize that your breed quickly becomes tightly related. After only two or three full generations you find yourself having to resort to inbreeding to further increase the numbers of specimens. So what exactly happened? And why could this development potentially be a bad thing? And what is inbreeding anyway? Before we proceed, let us first briefly discuss the terms inbreeding and linebreeding.

    In the canine world, inbreeding is defined as breeding closely related dogs to each other, i.e. parent to offspring (vertically) or brother to sister or half-brother to half-sister (horizontally). Let me stress right away that inbreeding in itself can be a valuable tool to "fix" certain desired genes and should not be quickly discarded as the works of unethical breeders. This writing is really not supposed to become an argument for or against inbreeding, rather a plea that a full appreciation of its broader implications should be paramount before even considering such a breeding strategy.

    When we now look at the term linebreeding, it is traditionally referred to as a relaxed form of inbreeding, meaning the matching of distant cousins or aunts to nephews, grand-uncles to grand-nieces etc. In reality, the distinction between those two forms of inbreeding is just arbitrary, as genetically speaking there isn't a fundamental difference between them. Emotional reservations aside, the actual genetic relationship of two individuals is scientifically determined by Sewall Wright's Coefficient of Relationship (RC), which basically computes a percentage of relatedness by derivation from the Coefficient of Inbreeding (COI).

    I'll spare you the math. But it turns out that solely based on their four generation pedigrees, apparently unrelated or only remotely related dogs from the same breed can share a substantial amount of common genes, resulting in a notably high inbreeding coefficient, when mathematically verified over the past 10 generations. This is actually the case for the vast majority of today's purebred dogs. Inheritance is not as straight forward as many believe. Oftentimes, people mention percentages of "blood" in their dogs as if these were absolute certainties, whereas in reality the percentages beyond the actual parents rather describe only probabilities. Believe it or not, this is an important distinction.

    There is no physical law that makes sure that a pup is 25% genetically identical with its grandfather. This is only the probabilistic mean, to be observed if one would fully genotype thousands of puppies and their respective grandparents, then calculate the average similarity; it's just a convenient simplification that works somewhat well in practical terms nothing more. Please keep in mind that these numbers are only an abstraction of reality.

    Ok, now that I sufficiently clouded the neat and cozy Mendelian approach, let us get back to quantitative genetics, or at least a global viewpoint. As various dog breeds evolved over time, people had primarily the same principal objective, to obtain sufficient consistency in the progeny of their dogs with regard to some defined labor task. They strived for a distinct conformation in phenotype as well as certain favored personality traits; in short, the optimal dog for a given task. When we really think about this from a genetic perspective, the underlying objective really was to limit the variability of a given gene pool in order to create a coherent type of dog, that performed well above average in the respective niche.

    In this procedure, an initial dog population of some intrinsic diversity would be progressively "pruned", until a new dog population of superior working quality had been obtained. Just as the consistency in phenotype improves, the variability in the offspring decreases over time, meaning that the range of available alleles in the gene pool narrows over time. A while ago, I started a MolosserDogs thread with the title “What is a mutt?”, only to illustrate how people would struggle to clearly define what the criteria for being a mutt would be. I believe that there is no clear cut definition. If anything in that regard can be said with confidence, then it is probably that purebred dogs display a tighter genetic variability than "mixed" dogs.

    By the way, the consistent phenotypes due to limited gene pools with homozygosity for many alleles in pure breeds are of fundamentally different composition (and quality) than those of wild pariah dog populations. This has to do with masking of recessive genes, which unfortunately is beyond the scope of this topic. Only this much, in gene pools of pariah dogs, recessive genes can be carried along without being frequently expressed nor completely eliminated from the gene pool; only to pop up, if and when they prove advantageous. Anyway, as far as we are concerned for now, whenever we study the gene pool of a particular dog breed, it is safe to say that we are dealing with a more or less isolated subset of available gene alleles from the generic gene pool. Now, narrow and isolated gene pools aren’t an exclusive phenomenon of dog breeds created by man. Small wolf packs in nature for example aren’t exactly fully transparent either, their sexually mature members are certainly not available to every potential mate out there but restricted to selected specimens even within their own family. While close incestuous pairings seem to be the rare exception in wolves, this arrangement still meets the criteria for loose inbreeding. If what we call “linebreeding” constantly occurs in nature itself, it can’t be all that bad in breeding programs either, right? Yes, of course. But there's more to it.

    Let us come back to this issue a little bit later. When linebreeding is performed in a meaningful manner of strategic breeding efforts, the objective is to emphasize desired features or to eliminate undesired genes. Inbreeding is used to "fix" specific genes, essentially an attempt to concentrate the allele frequency of a targeted trait. This is a science in itself and the subject has been satisfactorily discussed in other threads already. I would only like to discuss the "side effects" here. Due to affects of gene linkage, we cannot pretend that we are solely tinkering with the targeted gene, when we try to modulate an allele frequency of a population to our advantage.

    When we fix one gene, we affect others in their relative occurrence as well. Without even realizing it, we are likely to increase the rate for infrequent recessive defects that just happen to be closely linked to our original gene of interest. One might now hastily conclude that all inbreeding (whether incestuous or line-breeding) is "evil" and simply resort to selecting very distantly related specimens from the same breed. Let us investigate this potential strategy for a moment. I hope you still remember our initial thought experiment. Let us switch into the next gear. Suppose we are dealing with a rare breed of about 400 specimens total, which are unrelated. (I use 400 as this is the number that Gary Sicard came up with in a recent discussion. I will demonstrate shortly, how the exact amount of specimens in a breed is almost irrelevant.) For simplicity, we will assume that about 50% of these dogs are male, the other half obviously female; none of them spayed or neutered. How long do you think, will it take before all dogs are related to each other? If you guessed after eight generations, you are right. This seems so counter intuitive, doesn't it? The reason for this rapid decline in unrelatedness is that the genetic convergence follows a logarithmic function.

    For those who are interested, the equation to determine the first generation of inbreeding is Gi= |(ln(n)/ln(2))+0.5|+1 , where n is the amount of dogs from the less represented gender. What this really means is that the possible number of available unrelated specimens is cut in half with each generation. So, if we had just 16 studs and equally as many females, we'd experience unintentional inbreeding within only 5 generations. And keep in mind that this would only hold true, if one employed every specimen equally in the breeding program. If any stud were to be favored as a show champion for example and all bitches were bred to that one stud, then complete relatedness would obviously be achieved much sooner; this could be considered as a founder's effect. The subsequent unintentional inbreeding would further amplify unwanted traits or more precisely, genetic diseases. And in fact, this is precisely what happens in so many "novel" breeds. The genetic base is so thin that it usually takes only 10 years or less in a breeding program, until more and more problems surface within the breeding stock. A perfect Pandora's box, as far as I am concerned.

    I have previously mentioned that narrow gene pools are not bound to man-created dog breeds but also occur in wild populations of canidae. If these effects are as detrimental as I make it sound, why aren’t wolf populations riddled with genetic diseases? Why do breeders and dog owners experience problems more frequently in recent decades and not as severely in the early days of breeding for type? The answer to that is that "line-breeding" is only one half of the story, only one part of a truly successful strategy. When we look at wild predator populations, one thing becomes immediately apparent. Let's assume an ecosystem of stable equilibrium between a population of some sort of prey and a pack of wolves. A female wolf comes in heat only once a year, and even then on average she produces around 25-30 young wolves throughout her life.

    However, in order to maintain that aforementioned perfect equilibrium (I will refrain from harmony, as the prey would probably beg to differ), statistically speaking, all she really needs to produce are two new wolves, one to replace herself and one to replace the sire. This progeny would maintain the wolf population stable, until the next generation eventually takes over. So the legitimate question is, what happens to the other wolves? It is well documented that the majority of the offspring will simply starve or die prematurely of other cause. Bluntly stated (and statistically of course), only the fittest survive. Nature "recalls" those that didn't make the cut for whatever reason.

    I was recently asked, if it was true that historically, livestock guardian dogs such as the Sarplaninac truly had only very few puppies in a litter? The suggested 2 or 3 puppies per pregnancy would indeed be remarkably low, considering that those sheep guardians are pretty large dogs. My response was that I'm sure that in many cases only very few puppies officially made it to young adulthood, regardless of how many puppies the dam actually gave birth to.

    Well, these were different times and not all dogs in a litter were necessarily allowed to live long and prosperous lives. Even at older ages, dogs that didn't perform as expected, were simply culled, no questions asked. Such a strict breeding regime ensured that only the toughest dogs survived; those with genetic impairments didn't make the cut. Almost like the unfit wolves. Today, mentioning the word culling is almost a strict taboo. Yet, it is necessary to complement systematic breeding efforts, whether we like it or not.

    Now, before breeders rush off into the garage and get their big axe out, I would like to stress that I am IN NO WAY suggesting any killing of puppies. While people in the past supposedly did not know any better or didn't have the means, today we have the privilege to have modern tools at hand that would allow breeders to cull without actually harming the individual dog. Recall that the real objective here is only to eliminate unfit phenotypes from the gene pool, not to harm dogs. The overall goal of such an endeavor really should be to improve the health of the intact population as a whole. Modern tools could be comprised of spaying/neutering, limited registration, withholding pedigrees until breeding age, shared ownership etc. Responsible breeders should first and foremost keep the well-being of the breed in mind. Such an effort can only be a bottom-up approach and not dictated by breed registries.

    In conclusion, line-breeding techniques are unquestionably useful in a breeder's aspirations to produce better dogs. Incestuous inbreeding, if applied correctly, can be very effective in fixing genes of interest. However, these techniques require very close monitoring of the offspring, in particular for undesired traits and harsh culling.

    People are frequently unaware of how quickly a given dog population converges into a single cluster of interrelated specimens. This occurs at a much accelerated rate, when breeders all eagerly breed to the same show champion. This can cause problems rather sooner than later. It is therefore a myth that all puppies from reputable breeders will be of outstanding quality. This viewpoint may be lucrative for the individual breeder, but let’s face it, not all puppies should be bred down the road. If culling is omitted for financial or emotional reasons, all that people are really doing is to support the increase of genetic problems for future dog generations. I realize that I have only scratched the surface of many issues. I did not aspire to achieve even remotely thorough coverage of this complex matter.

    But I hope that I could at least provide some rationale, why breeders should start seeing the breed in a big picture, and especially the potentially detrimental effects that their own actions might have for the entirety of the breed. There will surely be those who will utterly refuse to accept the importance of culling as part of a comprehensive breeding strategy and I understand that this can be a controversial issue. Nevertheless, IMHO it is part of the equation. Or just as the novelist and philosopher Ayn Rand put it, "The way to kill greatness is to elevate mediocrity."


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    • Provocative article and thanks for posting.....

      I cull pups, humanely (vet puts them to sleep), and always have, even back when I was raising Catahoulas (mostly white headed pups were usually deaf so were put down). I have culled recently for a bad bite and a little female puppy that had a hip damaged in the womb and never outgrew it, and by six weeks it was obvious, she'd be lame. The rest of the pups in the litter made the cut. One had borderline overshot bite but vet said he was confident his adult teeth would come in better so he went to a wonderful home up in Oregon.

      I have a female Spanish Mastiff with bad tibias (note: out of HD rated A parents too, so much for saying A hips = no problems, not hardly)...that developed when she was around 4-5 mos old. I won't breed her in spite of the fact that she's a massive, beautiful girl - I would not dare chance that she'd throw even one pup with bad rear knees or legs. Her hips were good (we x rayed), it's down lower in her left rear leg. Anyway, she can get around well, is an excellent guard and goat guardian, and is my 'house potato' who gets to sleep in the house when she wishes. Breeding inferior dogs together will only produce inferior specimens. Soundness is so important.

      But so is type. Breeding say, a Spanish Mastiff of very little type, skin and wrinkle to another like dog, will only serve to take away some of the breed's most cherished characteristics. If in turn pups from that cross are bred to likewise less typey dogs, soon, you are breeding oversized Labs....or a facsimile of one! And losing cherished points of a true mastine.

      There has to be a balance. I had another SM female I opted not to breed, due to lack of type, size, and an unpredictable and somewhat sullen temperament. Plus, she chased and mauled goats. Was out of working dam too. I gave her to another rancher who has her more for a pet and house guard not livestock guardian. And, three of the best guards I have here in SM's are out of show ring stock, that don't work. But their pups are fabulous top notch livestock guards. Go figure.

      I think outcrossing is key now and then to any successful breeding program and hybrid vigor cannot be denied when you cross breeds together for F1 crosses.

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      • I wonder how much of the hybrid vigor is based on the placebo effect. Thanks for posting your honest reply and telling that you do make choices based on your knowledge of your litter. I wish more breeders would do that. Especially, those who breed Neapolitan Mastiffs.
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        • Thank you for this post. I have culled in my litters, often if you watch the dam she will also que to any unfit pups as well, be it out right rejection of one or two pups while fully excepting all others, or just a little less attention on her part to the pup in question. If you wait and watch those pups you will see that they are weaker, or in one case of mine actually had a defect in her digestion, that we found through an exam with my vet. Many people would not want to know about a culls in a litter, but the dam and the remaining pups are always healthier for it. And I feel ok knowing that no future families will have the heartache of dealing with health issues in the future. And the dog will not be in distress or pain. Thank you again for this post, and yes culling does not always have to mean actually ending the pups life, spay, neuter and many other methods are helpful. It's case by case every one is different.
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          • very good article- i think inbreeding coefficients should only be taken as a rough guide though e.g say a greyhound can run 525 yards in 28 seconds and none of his siblings can break 30-then the faster dog obviously must have a very different genetic makeup  and realworld inbreeding coefficient to his siblings.


            Do you guys think sex balancing is important? i.e pups descended from a desired ancestor through both daughters and sons on opposite sides of the pedigree.

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            • This post it to bump this wonderful article posted by Dan on our original site. Dan is a world renown geneticist who was a frequent poster on our forum and a breeder of the Sarplaniac dogs.

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              • This is a great article. I agree with culling and line breeding. Every dog that has a litter can and will produce dogs that will not meet the standard for the breed whether that is the conformation and or function for the breed. That does not take away from that pup being a great dog or great companion. It can be the best working specimen you have, but it should not reproduce as it can and will reproduce other dogs that has the same or similar issues that it has.

                I met an AKC judge at a dog show. He was showing his Black Russian Terriers. It was a rare breed show. He said something to me that day that shocked me because he is an AKC judge. He said if the mother rejects a pup he will do the same. He will not bottle feed and or try to save it. There is a reason why the mother has rejected it. It need to be cut off from the gene pool. I had never considered that. While I can't say definitively that he is right or wrong, but it gave me something to think about.


                I know breeders that have bred dogs with known genetic faults. Some of the faults were major. Then tell me that the pups turned out fine. My concern is not just for the pups from that dog but now all of those pups carry the traits to reproduce these faults in future litters. In my opinion those dogs should have been removed from the breeding program. I also have a friend that is a breeder. He had this dog that is a champion of record. She was a beautiful dog. She died not too long ago at the age of 16 or 17. There were many people that had requested a pup from her. There were number of other breeders that want to breed to her. Many told him that he should breed her. But he refuse to breed her. She lived her life as a pet on is place. He didn't like something about her rear end. So he did not not her reproduce this in future generations.


                I don't believe you can have a breeding program with consistency without line breeding. Since it was mentioned regarding inbreeding I will say this. Line breeding is inbreeding. I don't say it for an argument. But the reality is it is still inbreeding It just sounds nicer when we say line breeding. While I agree there are some benefits to inbreeding a mother back to a son and brother to a sister, etc. It is not my persona preference to do this.


                I try to look at the whole picture when breeding. I am trying to get away from saying my interest is in improving the breed. I know that sounds awesome that you want to improve the breed. To this this that would mean to change the breed. Personally I want to maintain the standards that were already created. I want to produce dogs that have the correct conformation as well as the correct temperament for the breed. I want to produce healthy dogs. I want to achieve the consistency in my litters. I love hearing from the vet that there are no runts in my litters and they are all consistent with each other.


                Pedigree indicates what the animal should be

                Conformation indicates what the animal can be

                But performance indicates what the animal actual is

                As stated in the article that we should consider the COI when breeding. But it is still probability.


                The article also mentioned wolves. We all know wolves are not dogs. Yes they share some genes. They are closely related. One other reason that I didn't notice being mentioned in regards to why wolves to have all of the same genetic issues that we have in dog breeding. There were things we once believe were true concerning wolves that have later been found to be incorrect. We have used this misinformation and have applied them to dogs and their behaviors as we claim wolves are dogs ancestors. Wolves for the most part do not have humans determining who, what or when to breed. The gen pool is limited. But in a wolf pack much of these problem do not become issues is because in a wolf pack there is not an alpha male as once believed. There is a breeding male and breeding female. There may be other males in the pack and they have a role in the pack that helps the pack survive. But there is only one male breeding. Therefore that male is the only male passing on it's genetic traits.


                The term alpha wolf male and alpha female was made popular because of what was written by wildlife biologist L. David Mech's 1970 book The Wolf: The Ecology and Behavior of an Endangered Species. The book has been reproduced and is on paperback. He has since changed his stance after further research. Initially his finding were based upon wolves in captivity. But later after studying wolves in the wild he discovered that there was no alpha male and alpha female. It was parents and their children that made up a pack. He has since rewritten the book to contain more updated information but the publishers were not willing to reprint it. Most of what we know about wolves were based upon his misinformation. There is a lot of research on this. Below is just one link on the topic. I won't go too far into this as that can be a completely new topic.

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