Wild canines do live in dens, but only for short periods in their lives. The wild behavior is similar to a whelping box used for newborn puppies. While crate training is often compared to the denning instinct in dogs, there's debate about whether crating is a humane practice.
Wolves, African wild dogs and coyotes all use dens. The mother animal seeks out a den during the latter days of pregnancy. This will be the safe space in which she gives birth to and nurses her vulnerable newborns. However, by the time her babies are a few months old, both she and they will abandon the den and live above ground, sleeping in the open with the rest of the pack. Among some canine packs, the father or other members of the pack will guard the den while the mother is nursing. Other pack members may bring food to the mother and babies while they're in the den.
The use of a whelping box for an expecting dog is similar to the denning behavior seen in her wild kin. The human guardian of an expecting mother dog places a box in a quiet, secluded area of the home a week or so before the puppies are to be born. The box is large enough for the mother to stretch out for nursing and high enough that the puppies cannot crawl out. It's a size that allows the mother easy access to and from the box. She'll give birth in the box and nurse her babies in it for the first few weeks of their lives.
The use of crates for dogs is often defended on the basis that dogs naturally seek out a den in the wild. Crates are used for house-training and for confining a dog when it can't be directly supervised. The use of crates are advocated by many humane organizations, including the Humane Society of the United States. Most of these organizations do stipulate how long and how often a dog should be crated in order to ensure the cage is used humanely.
Among those organizations opposed to the use of crating is People for the Ethical Treatment of Animals. PETA denies that dogs are naturally denning animals and points out that wild canines only use a den for about the first eight weeks of life. Even then, according to PETA, the den doesn't have a locked door, so the animals are free to come and go as they please.
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