Scratching at bedding is just one of those odd things that dogs do. They also turn round and round before lying down. There is a general consensus among dog behaviorists that both these oddities are a remnant of the dog's wild heritage.
Just as we smooth the sheets and fluff the pillows on our beds, dogs have the urge to rearrange their bedding for greater comfort. Digging, circling and trampling may have once shifted sticks, stones, leaves and grass into a position more to their liking. Charles Darwin cited this behavior of the domestic dog as an example of vestigial behavior, an action that persists after it has become useless or irrelevant.
Another possible interpretation of the bed-scratching activity is that the dog is attempting to dig a den to hide in. In the wild, circling would result in flattening tall grass, both to form a comfortable surface and to conceal the animal's position. This behavior is, of course, futile when practiced on a firm, flat surface such as a modern dog bed, and could therefore be seen as vestigial.
Scratching could also be an attempt to achieve a more appealing temperature zone, either warmer (by removing snow) or cooler (by reaching a cooler stratum of earth). Dogs often dig such holes outdoors, and may repeat the behavior vestigially indoors.
Bed-scratching in a pregnant bitch is called nesting, and may be a sign that she is about ready to have her puppies. In this case the behavior is not vestigial, but hormone-driven.
As long as the dog scratches only at his bed, there's no problem. However, if he starts seriously digging on your wall-to-wall or the orientals, it's time to step in. Give him a rug or a blanket in his favorite spots so he can rearrange the bedding to suit himself. Teach him to use his bed(s) and no other areas for sleeping. Confine him to a floor he can't hurt -- with his bedding, of course. In the case of the whelping bitch, make her a nesting box full of clean rags, newspaper and other soft, disposable materials early on in her pregnancy and encourage her to nest there.
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