Why does inbreeding cause deformed puppies?
Inbreeding does not automatically cause deformities or defects. What happens is that the closer or more often you inbreed, the more likely the parents are to carry the same genes. If the genes are good ones, then you get really good dogs. But if the parents each have a recessive gene for a problem, then it is likely that some of the puppies will have that problem, and most of the rest will be carriers. This is why it is very important to have a good knowlege of genetics, the inheritance modes of genetic diseases and the dogs involved and their families before attempting inbreeding. And you must be willing to cull anything that is defective. Done properly, inbreeding can actually be used to eliminate genetic diseases. There are now strains of disease-free laboratory mice which have been carefully inbred for many generations and selected for health and vigor. Control of Canine Genetic Diseases by George Padgett is an excellent book on the subject.
Lack of genetic diversity. When you are faced with a small population, any population such as a secluded herd of sheep on one small mountain peak, they eventually run out of different partners to pair up with. So eventually you have brothers and cousins interbreeding. It is actually natural in small populations especially ones that are endangered. However when it comes to dogs people breed them for certain traits and temperments and forget about the generations and relationships among their breeders. So they end-up inbreeding. They think it will produce better puppies with cuters faces, better stances, or longer noses. When this happens you are limiting the gene pool or limiting the genetic diversity amoung your population. So instead of the perfect puppy you end up with genetic deformities or anomolies popping up in the DNA. This does happen naturally, and explains why there are genetic disorders in humans, it is not always inbreeding, however when certain pieces of genetic code conta