 -- Family pets may be cuddly friends, but their gradual transition from the wilds to the hearth offers a sobering message: tampering with mother nature can have totally unexpected consequences.

Ever since that first wolf sheepishly sought the companionship of humans -- and their scraps from the dinner table -- people have selectively bred everything from pigs to horses to see if they could tailor the beast to be a better servant.

Those early experiments with genetic engineering created animals that are vastly different from their ancestors in the forests, and for more than a century scientists have been trying to figure out why.

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Even Charles Darwin couldn't explain something he called "domestication syndrome," dogs, foxes, pigs, sheep, and many other animals change dramatically when they become partners in the human pageant.

The question is: "Why?"

Why do most dogs have floppy ears, while the only animal in the wild with floppy ears is an elephant, according to Darwin's research in the 1800s?

Why do so many domesticated animals have white patches of fur, called depigmentation?

Why do so many pets have smaller brains than their ancestors, and smaller jaws and shorter snouts and smaller teeth?

Darwin thought there had to be a common cause for all those changes, although they seem so unrelated. Down through the years scientists have offered a number of theories, but none have been universally accepted. Now, scientists in Germany, the United States, Austria and South Africa have zeroed in on a biological process that begins very early in the embryonic spinal column of vertebrates.

The theory suggests that selective breeding causes some stem cells in that region to malfunction, or even get lost on their way to the part of the body where they were supposed to begin building tissue like that found in the wild.

In other words, this early experimentation with genetic engineering produced some results that no one had anticipated. Like floppy ears.

"The history of breeding is rich in this sort of thing, you breed selectively for one trait and often get something unexpected that is linked to it in some unanticipated way," Adam Wilkins of the Institute of Theoretical Biology in Berlin, lead author of a paper in the journal Genetics, pointed out in an email.

He added that the results were not all bad, even if unexpected, because we ended up with furry companions that in many cases have changed human history.

But doesn't this offer a warning to geneticists as we enter uncharted territory in tinkering with the blueprints of life?

"Whether of the ancient form of selective breeding, or more modern forms involving all the latest genetic-molecular modifications, do we need to be aware of possible unintended consequences? That strikes me as absolutely valid," Wilkins said.

Wilkins, along with co-authors Richard Wrangham of Harvard University and Tecumseh Fitch of the University of Vienna, argue this all began thousands of years ago, perhaps when humans first noticed a wolf that was very different from other wolves. This guy wasn't afraid of humans. He wanted to be a hunting partner, and a companion.

That isn't a frivolous idea. It's likely wolves were the initiators of the domestication process. They had much to gain, because humans have probably always left a lot of food lying around after the hunt. So why not join them?

But that suggests that those first volunteers were different, less likely to be pumped full of adrenalin and struggling with "fight or flight." The adrenal gland, which supplies the adrenalin that prepares the body to spring into action, begins life in the same area pinpointed by the researchers as the likely source of the "domestication syndrome."

Perhaps those early wolves came up short on adrenalin. The adrenal gland is formed by a group of stem cells called "neural crest cells." These cells also migrate to the various areas of the animal, as it grows from embryo to living beast, where the changes between wild and domestic animals are most apparent.

The new theory suggests this: If all the cells don't reach the ears, they will be slightly deformed, or floppy. If some arrive at the jaw in a weak condition, the jaw would likely be smaller. And some errant cells could cause depigmentation, that white chunk of fur on fido's chest. And so on.

That's the only known theory that cites a single biological cause for the changes seen throughout the domesticated world.

Initially, wild animals were bred only for tameness. In recent centuries they have been bred for many reasons, including cuteness among dogs, and speed among horses.

Surprises like floppy ears were unanticipated, but were they a bad thing?

"I think not," Wilkins said. "In the case of domesticated animals, most of them would not survive very well in the wild if they were released, but in captivity they do perfectly well and while the traits of the "domestication syndrome" are technically defects, they do not seem to harm them.

"And for us, the domestication of animals was a major advance that made the development of our civilizations possible," he added, "or at least they contributed substantially to that."

What would farmers have done without beasts of burden? And how could we get by without our furry friends?

In this particular case, I suspect most of us would agree that the "domestication syndrome" isn't entirely bad. Our dogs even look friendlier.

But one fact should not be overlooked. This was not the intended result.

It's likely there will be many other experiments that will produce surprises, and not all those stories will end happily.