a biological perspective on mutts and purebreds*

Many people are confused about issues related to the genetics of “purebred dogs” vs “mutts”. The words used to describe these dogs may in part reflect, or may reinforce, this confusion. People erroneously believe that mutts are somehow inferior to "pure"-bred dogs. Nothing could be farther from the truth.

Every dog is unique, of course, like every human, and each has his or her own special virtues. And many breeds undeniably have been bred to be exceptionally talented at certain tasks (herding, retrieval), or are exceptionally beautiful to those who admire their particular aesthetic. Golden Retrievers, who seem to appear in car commercials more often these days than beautiful women, come to mind.

The point here is not that purebreds are "bad", but that mutts have been given a bad rap, and that for overall odds of genetic soundness, mutts may in fact be the better bet.
The truth according to biologists is that “purebred” dogs are all more or less inbred, and are genetically disadvantaged, ON AVERAGE, compared to mutts. Purebreds are like certain Appalachian communities, or the royalty of old Europe: everybody is more or less related to everybody else. Even if a breeder jetsets around the world to find mates for her dogs, the mom and pop doggies are still going to be so genetically similar to each other that they might as well be cousins. All the “careful breeding” that responsible breeders do is an effort to counter the effects of inbreeding and avoid specific flaws that are inherent in every “pure” breed--- in other words, careful breeding does not produce offspring superior to mutts; it only seeks to alleviate the ill effects of purebred genetic limitations.
Breeds have been developed by selecting for a few traits out of the total diversity of the dog gene pool. This has had two kinds of harmful consequences for purebred dogs.

First, certain harmful genes that are rare among dogs in general have become abundant in particular breeds. Examples include von Willebrand disease, a disease that affects blood platelets (Doberman Pinschers), cataracts (Rottweillers & poodles), entropion, a curling in of the eyelid (Shar Peis), epilepsy (Belgian Shepherds, German Shepherd, and others), rage syndrome (certain cocker spaniels), or syringomyelia, in which the skull is too small for the brain (Cavalier King Charles Spaniels). These genes that can cause trouble do so most often by “doubling up”—by being inherited from both parents. Within a breed, many healthy individuals carry the same defective, recessive gene. If two apparently healthy dogs with the same recessive gene are bred, there is a 25% chance of any of their offspring having a double dose of the bad gene, and thus suffering the condition it causes.
Breeding most of these recessive genetic diseases out of a breed is difficult because the defective genes are hidden in apparently healthy parents. Some defects are bred for, though, like the “dappled” or “merle” color pattern caused by a defect in a pigment-producing gene. Individuals with one copy of the gene have an attractive color pattern, but those with two copies of the gene often suffer blindness, deafness, or fatal problems.
Among mutts, on the other hand, when a harmful gene is present, there is a much larger probability that it will be balanced by a beneficial gene for the same trait, coming from the other parent.
The second way that purebreds are genetically disadvantaged springs from the fact that many breeds have been selected to have peculiar body types that mark them as “distinctive” but are not suited to success as a dog: exaggeratedly small or extra-large body size, each with built-in problems; or very narrow craniums, etc. This leads to health problems, e.g. back pain in Dachshunds and Corgis or severe, even fatal breathing problems in flat-faced dogs like bulldogs.
Many of these peculiarities started out as actual mutations—genetic abnormalities that someone thought were cute or attractive or just weird and different and therefore marketable. So, dogs with those mutations were deliberately bred and offspring who inherited the peculiarities were then bred some more.
Purebred dogs have potential advantages like predictably unusual shapes or behaviors, but these advantages come at a cost of lowered average genetic health. Of course, genetic health is individual, but one can safely predict that more mutts than purebreds are genetically healthy. Greater diversity in the gene pool, like diversity in cultures and in ecosystems, is healthier. Given the same care, mutts have a better chance of intelligence, health, and longevity than purebreds, on average.
“Designer mutts” are a recent trend that combines desirable traits of two breeds to produce a dog that now costs hundreds whereas in the past it would have been “free to a good home”. In terms of genetic soundness, these dogs are likely to be midway between purebreds and mutts—they will have more variable genetic heritage than purebreds, but more limited heritage than most true mutts.

* thanks to Barbara L Wilson, PhD, for fact checking