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Birth Defects
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When a litter of inbred puppies is born, they may have obvious physical defects. This can include imbalanced proportions -- an eye, ear or leg that is smaller than the other, or placed higher or lower. Their tails may be kinked or missing entirely, and they can have enlarged heads or cleft palates. This is a result of having the same recessive gene appear in both parents, something that is much more likely when those parents are closely related.
Size
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Inbreeding tends to cause low fertility in dogs, so they produce fewer puppies and those with low birth weights. They grow more slowly and even as adults are smaller. With continued inbreeding, this trait increases so that each subsequent generation has smaller litters and pups. Not only will they be smaller, but also less vigorous as well. In order to get them back up to the sizes that are normal for that breed, larger, unrelated specimens have to be bred in.
Diseases
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Once again, recessive genes combine in inbred dogs to produce a high chance of chronic conditions such as heart disease, respiratory failure, tumors or cancer. Heart defects are more common. Inbreeding results in lowered immunity, so that throughout their lives dogs will have frequent colds and other sicknesses. Some inbred puppies have so little immunity that they die in the first few weeks of life, before they are old enough to start receiving vaccines.
Particular to Breed
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Some breeds are known to be susceptible to particular health problems. The reason that so many varied and specific breeds exist is because of past breeding patterns. Unfortunately, the same genes that give a dog its distinctive appearance can also make it sick. One example is the cavalier King Charles spaniel, a highly desired and highly bred small dog that suffers from a painful condition called syringomyelia, where its skull is too small for its brain. German shepherds are prone to hip dysplasia and English bulldogs have genetic hip, heart, skin and respiratory problems.
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Signs & Symptoms of Inbreeding in Puppies
Inbreeding is the deliberate mating of closely related dogs. This is often done in order to "fix" a certain desirable characteristic within a breed -- the shape of the head, the coloring of the coat, the width of the shoulders. Sometimes this causes a breed to be strengthened, but if it is done too much, genetic defects are replicated until they become common and the resulting puppies are smaller, weaker and more prone to disease.