Genetic Diversity

Breeding for Genetic Diversity in Standard Poodles

       Since long before the first litter was born here, we have striven to utilise the most up-to-date scientific information and techniques to inform our decisions, in the hope that what we do and how it impacts the future strikes a good balance between giving the dogs we breed the best chance at good health and a long life while being capable of doing what the breed was originally expected to do, and benefiting the long-term survivability of the breed. Initially, this has involved mainly pedigree analysis in the search for poodles whose ancestry is underrepresented in the breed as a whole and in need of preserving, and more recently as we have been able to assist with international research into the genetic diversity of the breed, more precise tools have become available, such as the Genoscoper study and the VGL genetic diversity test for standard poodles.

       Rare native breeds (farm animals) and dog breeds face similar problems when it comes to diversity, although usually this occurs for different reasons. With a breed such as the West of England goose, declining overall numbers and finding sources of birds makes it difficult to ensure enough diversity gets spread around and lines are not lost (breeders will usually breed to keep what they want and eat the surplus, and many may have low computer literacy and do not advertise stock and hatching eggs). Pedigree data tends to be scant, and when sourcing birds it is rarely possible to know how related they are to other birds from different sources. As there is no official registry for geese, it is possible for people to outcross to different breeds, and as a result, birds may not be representative of the breed they are supposed to be or breed true.

       Breeds of dog may have larger populations, and usually benefit from extensive pedigree information so it's possible to have a good idea of how related one dog is to any other dog, but the main problem is limited effective breeding populations -- resulting from overuse of popular sires and the genetic attrition that occurs from certain lines being so heavily bred they come to dominate the breed, whereas others disappear over time. In this case, locating dogs genetically different from the mainstream and keeping the population as a whole balanced in terms of genetic contributions is the problem, whereas with geese, knowing how unrelated your stock is presents the main problem.

COI & Inbreeding

       The Coefficient of Inbreeding is a calculation expressed as a percentage that shows how related to each other an individual's parents are. As such, it is a mathematical estimate, a probability, of the heterozygosity of the offspring, with lower COIs being an estimate of greater heterozygosity and higher COIs being an estimate of greater homozygosity. Inbreeding depression has been scientifically proven to have detrimental effects on the health and wellbeing of individuals. When inbreeding is confined to small local pockets that are genetically disparate from each other however, this has little impact on the overall diversity of the breed, as individuals from different populations can be bred together to produce offspring with a low COI.

       The Kennel Club has implemented a COI database and calculator for matings. Personally, I do not find this database particularly useful, as the number of generations over which the calculation is run is not specified, making the result meaningless, and imported dogs are always listed as having a COI of zero, which clearly isn't accurate. The Poodle Health Registry has a database which gives accurate COI calculations over 10 and 15 generations and also displays the pedigrees of all the dogs recorded on it.

       It must be taken into account that the more generations the figure is calculated over, the more computing power is needed to handle the calculations, and 15 generations is pretty much the limit where we are at the moment. This doesn't take into account inbreeding events more than 15 generations back, which brings me to:

Bottlenecks

       Wycliffe was a Canadian kennel in the 50s/60s. The dogs were popular in the show ring and as a result of this and the widespread belief supported by scientific understanding of the time that inbreeding could be used to concentrate good traits, they and their descendants were bred very widely, and as a result have come to dominate the gene pool of the breed. The Wycliffe % is the proportion of a dog's pedigree that traces back to these dogs, and a reference to inbreeding going back beyond the number of generations we can feasibly include in a COI calculation.

       The majority of poodles from popular lines are in the 50% or more region of Wycliffe contribution. This is why it is important to make use of low Wycliffe lines in breeding programmes in order to prevent further loss of diversity. You can see the Wycliffe contribution expressed as a percentage for any given dog on the Poodle Health Registry database.

       Read more about diversity and the Wycliffe influence on the Standard Poodle Project.

       More recently, many people observed that some low Wycliffe lines, particularly of standard poodles bred to be the apricot colour, had their own bottleneck which was just as severe, but less common in the population today, due to the use of a few popular dogs in history, chiefly 'Vulcan Golden Light' and his son 'Alpenden Golden Sand'. This bottleneck was termed the OEA (Old English Apricot) bottleneck. More recently still, a third bottleneck term has been developed, MCB (MidCentury Bottleneck) which takes into account that the Wycliffe bottleneck tended to pass into the modern population through particular popular sires who were not 100% Wycliffe, and that this altered the contribution of certain forbears who lived in the 1950s.

Genetic Testing

       As previously explained, COIs and bottleneck percentages are probability estimates based on pedigree analysis. They are not actual hard data, and because of the way genetic material is passed between generations packaged into chromosomes, the estimates can vary from reality and dogs can be more or less diverse than their pedigree information might suggest. There is also the possible issue of pedigrees containing accidental error, or occasionally deliberate fraud, and the possibility of bottlenecks that occurred before the breed was officially recognised and pedigree records began, since poodles and similar water-dog types were a landrace breed and existed before the formal concept of breeds was created. For all these reasons, we have been assisting with research into DNA analysis with our poodles. In 2014, we sent mouth swabs from our dogs along with a number of other dogs in the UK whose pedigree analysis suggested they might be unusual to the USA as part of a study at the University California Davis. The data derived from the study was used to develop a genetic profile of the breed. For some years before this, we had also been sending DNA to the 'mydogdna' Genoscoper study, and the dogs we have submitted are available to view on their website. These studies are among the first of their kind to look at poodle diversity on the molecular level, and provide hard data on how heterozygous individual dogs and puppies from potential matings are likely to be, and thus are give an estimate of these factors based on actual DNA markers rather than probabilty to complement probability-based estimates such as COI and %Wycliffe.

Perspective

       For perspective, all breeds of animal and indeed all species trace back to a few founding animals. Gradually, over many generations, random mutations build up in a population and cause it to differentiate from its founding stock and other related species. The mutation rate in dogs is thought to be one of the highest in all mammals and this has contributed an enormous part to the adaptation of dogs into different breeds to serve different purposes alongside people. 15 generations as translated into average human timescales would take us back to the early 1600s and in the 15th generation there are 32,786 ancestors. The Wycliffe Bottleneck occurred about 30 generations back in the pedigrees of most poodles being bred in the 2010s. In human timescales, this is like being able to trace a person's complete family tree back to the Middle Ages, and in the 30th generation, there are 1,073,741,824 individuals -- well over a billion, and modern estimates suggest there were only around 300 million humans alive at this time. This is normal in all wild and domestic species, and is called pedigree collapse. Most people cannot trace their own pedigrees back 15 generations, and certainly not to the Middle Ages, and it is unlikely that most humans alive today, unless their parents are from obviously different races, have a 15-generation COI that is zero. Additionally, depending on a person's nationality, there are probably bottlenecks prior to this from invasions and wars where it might have been common for, say, a Roman military leader to breed with many females in the local population while travelling about.
      Additionally, there is now some research that suggests low levels of inbreeding, below the level of cousin matings, may actually confer benefits to individuals, although obviously this does not excuse people breeding together half-siblings and other obvious recent relatives. Current thought and knowledge would seem to support the idea that 15-generation COIs around the 7% level are acceptable and do not adversely affect the health of dogs.

Making informed breeding decisions, and making an informed decision when considering buying a puppy

       When considering a puppy, if the only information you have available is COI, it's worth stressing that the puppy's COI is what is important and not that of the parents. Two dogs each with high COIs can produce a litter with a low COI if they are not closely related to each other. As a general rule, the lower the COI, the better, although a COI figures tend to get larger the more generations they are calculated over. Inbreeding depression is generally accepted to become negligible at values below 7% (approximate equivalent to a cousin mating) but in practice when working with 15-generation it's not always straightforward to find combinations that produce numbers this low, especially when trying to avoid bloodlines that may have issues such as genetic disease and poor temperament, and benefits and risks have to be weighed against each other. A dog whose pedigree is highly influenced by one or more of the bottlenecks may be very similar to most of what is being bred, and a dog whose pedigree has a low influence of all of them may be rather different.

       Breeding practices come in and out of fashion and scientific understanding evolves as more evidence becomes available. In the time when Jean Lyle (Wycliffe) lived, the belief at the time, including that of the scientists of the day, was that heavy inbreeding and selection could be used beneficially to concentrate the virtues of the dogs upon which it was based. In a way, this was and is still correct, but the problem with it was the loss of heterosis coupled with the popularity of the Wycliffe dogs which eventually resulted in the swamping or loss of much of the other bloodlines around the world which prior to this existed as genetically heterogeneous islands with occasional transfer of genetics between. Throughout the 2000s and most of the '10s thus far, there has been a climate of opposition to all forms of inbreeding and linebreeding which has become quite extreme to the extent sometimes of hatred from the public directed at breeds and calls for their annihilation and extinction, and the glorification of mongrels. Now with genetic profiling becoming available, it is possible to take much of the risks out of linebreeding by choosing genetically dissimilar animals to mate together even if the pedigree suggests they are similar, and by selecting the most heterozygous offspring, or the most unusual offspring compared to the mainstream in order to preserve the most of a rare bloodline that might otherwise die out or be overwhelmed by breeding it into the mainstream. The majority of rare breed farm animals would have died out long ago without their breeders using a linebreeding strategy of groups of related birds enriched by an outcross every few generations to ensure different farmers have genetically distinct reservoirs that keep the breed as a whole diverse. It is hoped that in future, the attitude towards a great variety of different breeding strategies aided and supported by scientific understanding and genetic profiling may become more moderate and reasonable.

       The (largely) closed registry system most national kennel clubs have for dogs works as something of a double-edged sword. On one hand, some breeds which have been mismanaged for too long and are dangerously lacking in genetic diversity would benefit from a carefully considered outcross, but what is involved in getting permission for this and doing it is complicated. On the other hand, we are extremely fortunate to have enormous amounts of data on the ancestry of our dogs through these registries and the ability to calculate COI many generations back and have real information from this on the genetic health of our breeds and individual dogs. This is not the case with many other animal breeds. To compare to the example of West of England geese, it is easy to do an outcross if it becomes necessary as there is no real registry or requirement for what you can or can't call a West of England goose, but it is rarely possible to know how inbred your geese are to start off with, as records tend to be nonexistent or very lacking, and as a result of this when you are buying geese or eggs there is no guarantee they will even look like the breed they are supposed to be or breed true to type.

Hybrid Vigour: Ligers and Leylandii

       Hybrid vigour, strictly speaking, is a phenomenon observed when animals of different species are bred together to produce offspring, such as in a liger, mule, or zebroid. It also applies for plants, with the most notorious example being the invasive and obnoxious growing habit of the monstrous Leylandii cypress trees. Both ligers and Leylandii are like the majority of true hybrid organisms generally sterile and incapable of reproduction.

      Sometimes the term is used for what is more correctly called heterosis in reference to terminal crosses in the farming industry (a terminal cross is a cross-bred animal that exists solely for slaughter or production in intensive systems, and is of no use to breeding programmes; compare this with an outcross which is generally carried out as the first step of a breeding plan to introduce a trait or characteristic into an existing breed). If hybrid vigour as it applies to farm animals applies to mixed-bred dogs, it is unlikely to be something people would want in their family pet, as it tends to produce freakish characteristics such as enormous size, great strength, and exceptional fecundity. In the case of modern farm animals intended to produce large amounts of meat, milk, or eggs produced by crossing two different breeds, often that have been heavily inbred in order to produce the characteristics required in the cross-bred offspring reliably, many suffer quite hideously distorted anatomy, such as broiler chickens too heavy to roost or mate, and pigs with neurological problems because of demand for lean pork (those who like to uphold modern farming cross-breeding practices as some sort of paragon of genetic health should read Temple Grandin's article here). It's also completely possible for outbreeding depression to occur.

       With the rare exception of carefully-planned outcrosses carried out as part of a long-term plan to increase diversity or add traits to one of the parent breeds where subsequent breeding to restore type and select for the trait follows, hybrid animals are almost universally useless for subsequent breeding, as the two different 'halves' of the DNA in a very heterozygous individual get reshuffled after the first generation and are not passed on to offspring in a predictable way. They exist in the instance of farm animals to enter the intensive farming industry, and in the case of animals like mules to do a specific job. To make more battery chickens and mules, it is necessary to return to the breeds/species from which they were created, as cross-bred laying hens don't produce offspring that are high throughput layers, and mules when they are on occasion fertile do not produce offspring with the typical qualities of a mule.

What a Pedigree Means

       All breeds of dog have been developed to serve a particular purpose and have their own history. If we do not continue to maintain these breeds, there will be no breeds left, and no dogs to perform these roles. That means no large, confident dog for a police officer to rely on, and no suitable dog for an old deaf person who needs a small lap dog for companionship and assistance. Both these people would have to pick a random mongrel dog and hope it would work out. There are some people who believe that humans and domestic animals are abominations and should be made extinct. I believe that humans and the breeds that developed alongside them are all natural products of evolution as well as our history, and have as much right to a future in this world as does every other species.

“I have heard that purebred dogs are inbred and diseased, and I have been told to buy a mongrel puppy from a breeder as it will be healthier.”

       If you are at all concerned about inbreeding and health issues in purebred dogs, the best way you can help is by finding a breed suitable for your lifestyle and choosing to buy a registered puppy of this breed from a small-scale breeder who health tests and takes measures to avoid health problems and loss of diversity in the breed they are working with. This way, you are using your money to support the efforts of someone working to sustain a breed and combat inbreeding and disease, and you get a companion who is hopefully less likely to become ill. Someone who produces mixed-breed animals generally does not care about the survival of breeds and may even hold them in contempt (the 'mutts are better than breeds' mantra). The animals they produce are to sell in order to line their pockets, and not to continue a bloodline and preserve diversity in a breed.
       Currently there is a fad for crossing poodles with many other breeds, giving them ludicrous portmanteau names, and claiming the offspring inherit the poodle coat and some other characteristic from the other breed. The person who is thought to have started this fad has publicly stated that it was a mistake and that he wishes he had not done it. There is no guarantee that puppies will inherit the desired characteristics from either parent. Dogs resulting from poodles crossed with double-coated breeds frequently inherit both the shedding undercoat and the constantly growing curly poodle coat, resulting in a smelly, greasy coat that sheds heavily and becomes badly matted unless clipped very short. Health issues specific to either breed can also be passed to the offspring. It is also not necessarily true that mongrels are never inbred, since if there is no pedigree information there is no way of calculating a COI, or knowing if, for example, the parents of the puppy could have been brother and sister.

“All dogs are wolves/mutts anyway. Why should dogs whose parents are different breeds not be recognised as new breeds?”

a. A great many of the breeds that already exist are in danger of loss of diversity, and in some cases even extinction. These breeds all have stories about how they came about, and are living pieces of history. It is my firm belief that we need to help these breeds before we even think about 'inventing' new ones. It is surely better to work on improving the breeds we have so we can keep them for posterity instead of trivialising them by granting breed status to more and more meaningless and poorly-developed new breeds.

b. Most dog breeds as we know today are either the descendants of landraces (dogs of a geographical region who evolved in a semi-artificial way alongside the people there) -- and poodles are such a breed, as they descend from dogs used for hunting in marshland -- or breeds that were purposely developed over a great many generations by persons or groups of persons with a specific objective in mind. For example, the Dobermann is one of the more recent breeds we have today, and it is very much a manmade breed. It was created from a number of different breeds by Herr Dobermann, a tax collector who wanted a dog for a specific purpose that could not be occupied by the other breeds available to him at the time. Dobermann carefully bred and selected the descendants of the dogs he bred over many generations to be of a predictable type and temperament. This is a far cry from someone allowing two dogs to mate together with no real objective or proper reason and pretending the puppies are a breed and giving it a silly name.

It is currently thought that the ancestor of modern dogs of all breeds is the grey wolf. But a dog is not a wolf and a wolf is not a dog, and inferring anything about what dogs are 'supposed to be' from how wolves behave or are thought to behave in a wild environment is as nonsensical as inferring human nature from the behaviour of bonobos. A dog would not survive long in the wild as a wolf lives, and the small number of people who keep wolves or part-wolf dogs as pets will attest that they are not well adapted as companions for people. I do not see what wolves have to do with this sort of argument and why people keep bringing them up, and indeed it just shows how much poorer life on Earth would be if there were not the variety of dogs we have now to suit different personalities and lifestyles, and if the only 'dog' anyone could own was a wolf and how unsuitable that would be on so many different levels.

       Please note that there are occasional, scientifically justifiable cases for outcrossing, such as the LUA Dalmatian project where there is a clear objective to the benefit of the breed rather than just the inside of the breeder's pocket, and where breeders are careful to choose a compatible breed that will not introduce more problems. There are also some genuine cases of purpose-bred working dogs made from two or more compatible breeds, such as lurchers and dogs for specific sports. Persons breeding such dogs are likely to have a track record with the work they are breeding the dogs for in these cases, and if they are established will have a proven reputation of producing suitable dogs with achievements in their chosen field, or if they are not already established will have connections to people in that sport. If you are in the market for such a dog, you are likely to need to look hard to find one and the breeder will expect to see evidence that you are acquainted with the sport the dog is bred for and experienced enough to handle a dog of this sort. There are also some breeds that may be recognised by a separate registry, such as working sheepdogs and JRTs, or foreign breeds not yet recognised. Please research carefully if you are considering such a dog, to be sure this is a genuine instance, and be wary of buying a dog where there has been no proper attempt at keeping pedigree records over several generations, as in these cases it is impossible to tell how much inbreeding is behind the animal you are buying.

"If I buy an unregistered poodle, it's still a poodle. The pedigree is only a bit of paper."

       When you buy a dog registered on the breed register from a breeder, both the owners of that dog's parents MUST consent to the breeding. When you buy a dog not registered on the breed register (and this includes the KC's activity and obedience registers because the details of the parents do not need to be entered) you have no guarantee that the parents of this puppy are the ones the seller claims they are or that they were used with their owners' consent, or even that the puppy or the parents were not stolen from their rightful owners, or imported illegally from a foreign puppy farm. A bitch may only produce four registered litters between the ages of one and eight years old, by dogs who are not her first degree relatives (first degree relatives are for example, brother and sister, father and daughter); an unregistered litter could have come from a bitch who is over or underage and there is no way of telling how many litters she has been used to produce or how closely related to the sire of the pups she is. Even if you are sure the breeder is legitimate and the dogs are genuinely theirs, every time an unregistered pup changes hands for money, this provides an incentive for people to steal dogs to breed for an easy profit. Please do not perpetuate the cycle: only buy dogs without breed papers from a shelter or rescue organisation. If you are looking for a non-specific dog as a companion and you feel it is genuinely not important to you to have a dog of a certain breed, or you feel the piece of paper really does not matter, this way you can help a dog in need, and the rescue will have been able to assess the dog and give you a reasonable idea what sort of personality and exercise requirements it is likely to have. You can always add your shelter dog to the companion or activity register with a name of your own choice.

"I don't want a poodle but I like that they don't smell or shed coat and are intelligent."

       If you want 'something like a poodle' that isn't a poodle (and yes, this to me seems paradoxical and makes no sense) please research other breeds: there are a great many and all are a little different, meaning there must surely be one to suit any preference. If you don't like that poodles don't smell or shed, and don't present enough of a challenge to train, consider an Otterhound, a rare native breed. Irish Water Spaniels are also a rare native breed, and are beautiful dogs thought to share ancestry with poodles. The Portuguese Water Dog and the Lagotto Romagnolo also share ancestry with the poodle and have a similar coat, but aren't poodles. The Italian Spinone is a tall, large-framed dog with a shaggy coat, and the Curly Coated Retriever has a very typical sturdy gundog shape but a curly single coat.

"Animal breeders practice eugenics. Eugenics is bad because it was invented by Nazis and Nazis are evil. And it's not scientific and we know much better than to do that these days."

       Eugenics is the tenet of breeding together individuals with wanted traits, such as health, good temperament, and longevity, with the intention that the offspring will exhibit these same features, and conversely choosing not to breed individuals that have the opposite attributes in the hope that this will reduce the likelihood of the offspring having these unwanted traits. Eugenics was originally indeed a scientific theory that began with Darwin's Origin of Species and included many experiments that demonstrated very well that breeding together, for example, tall pea plants tended to produce tall offspring. This early understanding led to our more advanced modern understanding of genetics and DNA, and in some cases we have far more informative and accurate genetics tests that enable us to make great progress at preventing the animals we breed from having diseases and increasing the likelihood they will have the traits we want.
       Nevertheless, our current understanding of genetics (and epigenetics -- the interaction of environment with genetics) is very limited, and in many cases we do still have to rely on eugenic principles to make informed breeding decisions. For example, in the poodle, there are as yet no genetic tests for sebaceous adenitis, hereditary cataracts, or hip dysplasia. If we want to try to minimise the occurrence of these diseases, we have to use information on the dog's phenotype to decide if this dog is suitable for breeding or not. This is clearly not as accurate as having genetic information and ideally we should not have to rely on phenotype tests such as these, but at the moment it is all we have, and we need to keep collecting information on the occurrence of these diseases in order to provide researchers with genetic material so they can hopefully one day identify the genes involved with these diseases so we can have genetic tests for them.
       The reason eugenics is associated with Nazis is because the Nazis unfortunately tried to apply eugenic principles to people, sometimes for health and intelligence and sometimes for ridiculous traits such as hair and eye colour and religion, and used it as justification for mass murder. Because the Nazis abused the scientific understanding of genetics of the time does not mean it is wrong in itself and some of the principles still do not apply today. This is a logical fallacy, a Reductio ad Hitlerum. Also please note that making eugenic decisions on which individuals to breed based on health, temperament, and conformation, is not the same as choosing to breed together animals with gross exaggerations such as dogs with very short muzzles, which should probably be considered more dysgenics than eugenics. It is also very important for anyone breeding animals to have knowledge of more modern advances, such as the area of population genetics, which suggest that excessive selection will shrink the gene pool and do more harm through loss of genetic diversity.
       Therefore, if I decide a bitch is unsuitable to be bred and spay her because her hip radiograph at 18 months showed evidence of osteoarthritis, or her SA biopsy or eye test showed evidence of these diseases, or because she has a poor temperament; or I decide to slaughter and eat a turkey because it isn't big enough to go back into the breeding programme, yes, this is eugenics. But it's important to understand what that actually means rather than having a kneejerk reaction 'because Nazis and Hitler and genocide.'