Many look at pure bred animals as being better. They are pure, which sounds good. We have an idea that thy are better for some reason. In a way we are right. With a pure bred labrador retriever (for example) of high quality you know what you are getting. It will have a thick coat, otter tail, friendly personality, desire to please, high intelligence, etc. With pure bred ranchu goldfish you should not get any trace of a dorsal fin. A pure bred Abyssinian guinea pig will have the wavy, cowlick hair expected of that breed. A pure bred animal will have the traits we expect from that breed. But there are many issues that come along with this.
In order to have a pure bred line, you must limit the gene pool. This is what will cause the problems. Anyone who has taken genetics (and understood it) should have a red flag pop up immediately at this point. This smaller gene pool is less adaptable than a larger one. There are fewer variations in the genes and this prevents the animal (or plant) from adapting to any changes. These include environmental factors like diet, temperature, as well as many chemical factors.
In the case of dogs we have many breeds. To maintain them as pure we must not mix in other breeds. In the 'best' or 'highest quality' lines there are the features we desire in them and a lack of genetic problems (such as many diseases). However, this is only in the dogs in the immediate past of the line. This does not prevent problems from arising in this or many generations down the line. This is why so many breeds have a tendency toward one or many genetic defects such as hip dysplasia, heart and brain problems, blindness, deafness, and in some breeds all of the above. Some breeds are even more likely to have a problem than to be healthy. Yet we keep breeding and buying these animals. The shar-pei breed in the U.S. is derived from four individuals imported many years ago. That is an extremely small gene pool to create and maintain a population with. It is no wonder it is hard to find an individual that does not have skin or eye problems. Most breeds have a tendency for certain defects. Whether it is blindness in the Briard (recently used as a subject in an experiment that returned vision using a virus to implant the DNA to make Vitamin A, the lack of which was what was causing the blindness), deafness in the Dalmation, hip dysplasia in the Labrador Retriever and German Shepherd, heart defects in the Boxer, etc., these are all the result of a small gene pool.
The way this actually happens is a number of ways. One is by removing individuals from the parent population (all dogs, dogs of that breed, etc.), you cut the population size down considerably. This is creating a founder effect. The founder effect in nature is when a small population of a species breaks off reproductively and no longer breeds with that parent population. The genes in this smaller population are in different proportions than they were in the parent population. What may have only been 0.5% in the parent population can be 20% in this population, for example. This amplifies the frequency it will show up as a trait. So what would be a rare trait to show up in the parent population can become very common, even likely, in that reduced gene pool.
This is not reserved to dogs. This is seen time and time again in all types of animals that are pure bred. Mouth and hoof problems in horses are one example. Many times it is not a genetic disease that is the issue, but a tendency for other problems. Most commonly this is seen as less hardy individuals. In many types of fish the 'fancier' breeds, generally those most distant from the wild type, are much more sensitive than the wild type or those closer to the wild type. This can be seen in bettas, guppies, goldfish, discus, koi, angelfish, and others. The fancier and more distant genetically from the wild type, the less hardy the individual will be. In some cases there is a bell curve ranging from wild type to the most domesticated and altered breeds. In these cases the wild type is sensitive, as you progress to more domesticated and altered breeds they become hardier, but as you get closer to the most domesticated and most distant from the wild type they become more sensitive. So the slightly domesticated breeds are the ones that are the most hardy. This is the case with discus. The wild caught individuals are more sensitive than most domesticated breeds, but the very high end breeds that are bred very selectively are also very senitive.
The usual response to this is something to the effect of 'they are not actually that sensitive as long as...' followed by certain specifications on their care and/or diet. This is by definition more sensitive. If some breeds do not require these special aspects of care but this one does, it is more sensitive than those other breeds. If a breeder of discus (or goldfish, bettas, guppies, what ever fish is in question) takes pristine care of the animal it is altering that line. If a fish is given a 75% water change twice per day, waste is vacuumed three times a day (after every feeding), etc., the fish raised in these conditions will become acclimated to this. This also diminishes any differences in hardiness because all the offspring are raised in such superb conditions. So an individual that may not have done well at all can end up doing almost as good as the hardiest of its siblings.
Another aspect is the process of choosing which offspring or individuals to be bred. When given the choice of 30 fish, some will grow faster and be more resistant to any problems (such as pathogens) than other individuals, or may process certain nutrients better and therefore grow faster and may show more colors. However, these will not necessarily be the ones that have the accepted characteristics of the breed. But in order for the line to be of high quality, those with 'proper' characteristics of the breed will be the ones chosen to be bred, not necessarily the ones that are the hardiest. This leads to problems down the line. Unless the accepted traits of that breed always show up in conjunction with the hardiest individuals you can not breed for both hardiness and 'high qaulity'. The response to this can be 'they are bred for both quality and health'. If this is happening then they are choosing the healthiest individuals that are of the highest quality, which requires an even more limited gene pool. Rather than breed the healthiest individuals, they may take the top group and of those choose the ones that best fit the breed standards. This limits the gene pool even more and even faster than other methods. So although this generation may be relatively healthy (at least in the pristine tansk of the breeder) that does not mean that the negative results of this selection will not show up down the line, even within a couple generations.
Another thing to keep in mind is that these traits are not inherently 'high quality'. We choose what traits are to be considered high and low quality. Or, more likely, some one or some people a long time ago decided what a certain breed of dog or discus should look like. These decisions are not necessarily based on anything that has to do with the health of the animal, but what looks good to us (really them). But we read in our books and were told by the breeders that a discus should have a certain conformation, or that the coat of this breed of dog should be thick and short. These do not necessarily show health at all, and may have been chosen despite the health of the animal, but are still important criteria in our minds before we hand over our dollars.
There are healthy pure lines out there. But many if not most can end up doing more harm than good. And many of the healthy pure bred lines are simply good so far.
There is a reason why so many have seen time and time again that mixed breed dogs are healthier and much less likely to have health problems than pure breds. Not just genetic health problems, but they are even more resistant to acquired health problems. In general they are hardier and more adaptable. A small gene pool is specialization because it requires certain conditions to thrive. It lacks the ability to adapt to changes. So if the next keeper of individuals in this line of discus does not do daily water changes, or this breed of mouse does not receive twice as much protein as most breeds need, they will suffer for it. It has even been seen in some cases where breeders recognise the need for outbreeding and intentionally introduce new individuals in to a breeding line to ensure genetic diversity within that line. In dogs, some of the hardiest pure breeds are those that were developed recently and used an assortment of breeds to develop the breed. In these cases an assortment of breeds were used (which increased the gene pool from the start), but since the breed itself is relatively young it is still varied and still maintaining a large gene pool.
This is even true in humans. It has been shown time and time again in many cases of humans where the founder effect literally brought out otherwise extremely rare traits in very small populations. Albinism, third genders, hemophilia, and many others have been shown to appear much more frequently in smaller populations or when outbreeding is reduced leading to inbreeding (which has been the case in Royal families in Europe in the past). These amplify the frequency of these problems.
