Dogs have tremendous genetic variety: from a wolf-like ancestor, they have developed into thousands of dissimilar breeds (genetic evidence shows this “split from wolves” happened around 27.000 years ago.) The differences between “breeds” of dogs are both physical and behavioral. It’s important to understand at least a little about genetics to understand why dogs look and act like they do.Everyone who has had high school science probably understands that there are both “dominant” and ”recessive” genes. In human eye color, “brown” is dominant and “blue” is recessive. If you have brown eyes, you could have 2 dominant genes, (BB) or one dominant and one recessive gene (Bb). If you have blue eyes, you have 2 recessive genes (bb.) You get one gene from each parent.
Chromosomes carry genes. Humans have 23 pairs of chromosomes in each cell (except reproductive cells,) and dogs have 39 pairs of chromosomes. If two genes are located near each other on the same chromosome, you will probably inherit those genes together. 
That’s why some unusual traits seem to occur together. There is a famous study of foxes in Russia. They evaluated foxes for friendliness, and bred 40 generations of foxes with the intention of breeding friendly foxes (this study took 50 years.) The “friendly” foxes also developed different physical and biochemical traits than the other lines. They had floppy ears, different fur color, curlier tails, different skulls and lower adrenaline levels. The more generations they cross-bred the “friendly” foxes, the higher the percentage of kits with that behavior. The first generation had only a few friendly foxes; by the 40th generation 80% of the kits were friendly. Why do physical traits accompany the behavioral traits? The genes for behavior and the genes for appearance are on the same chromosomes.
There is another wonderful experiment done by the Dog Genome Initiative, started in the early 1990s. They started with a male Border Collie and a female Newfoundland (a) – pictured below. The physical and behavioral traits of these 2 breeds are quite different. They compiled a list of 31 behavioral traits that were different in each of the parents. Newfoundlands (by nature) don’t crouch, don’t maintain eye contact with the owner, don’t react to unexpected noises, and aren’t awfully biddable. They love water, have a high demand for affection and are extremely social with other dogs. Border Collies are pretty much the opposite: they crouch, have a strong eye, are highly reactive, are biddable, aren’t attracted to water, like work more than people, and aren’t social, particularly with other dogs. They bred the dogs to each other, and observed the next generation (called the F1). The first generation pups were mostly black with a little white, larger than a Border Collie yet smaller than a Newfoundland, had a mixture of behavioral traits (for example, would both chase tennis balls and swim) and were strikingly similar to each other. Crossing puppies from this generation
to produce an F2 generation produced quite a different result. Some of the F2 puppies were bigger, some smaller. Some were black, some splotched with white. Some liked water, some hated it. Some made eye contact, some didn’t. Interestingly, “crouching”, eye contact and “work drive” did not occur in the same dogs (so probably aren’t on the same chromosome). Why did this happen? Some of the F1 generation pups had recessive genes for a particular color, size or behavior, and when 2 dogs with the recessive gene EACH passed that gene on to the next generation, that gene expressed and voila! The behavior or appearance changed.
So, what happens when dogs are “selectively bred” for a particular color, size or behavioral trait? Other genes (that are on the same chromosome) get passed along as well. I don’t really believe that German Shepherd breeders wanted their dogs to have hip dysplasia, they wanted a long, sloping spinal column. Golden Retriever breeders didn’t want their delightful dogs to be nicknamed “Cancer Retrievers,” but the incidence of cancer went up astronomically when the dogs were inbred for appearance. Pugs can’t breathe on airplanes, Boxers have seizures…..the list goes on and on. Dogs “bred themselves” for tens of thousands of years, and did a pretty good job of it. We humans have to be extremely careful not to let our desire for a unique color, size or behavioral trait in our beloved dogs to destroy any breed.
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