While many of your dog's wolfish instincts have been greatly reduced, others remain and explain much of her innate behavior. A dog's instincts can dictate valuable responses or annoying over-reactions. Among the innate behaviors with the highest importance is the domestic dog's need for social structure.
Dogs and wolves have long been the subject of studies of behavioral differences. Certain studies examine similarities between dogs and wolves, while others locate gene mutations responsible for the differences in behavior. As do wolves, domestic dogs prefer packs, although a domestic dog may be just fine with being part of the human pack. Wolves live in packs that have distinct social hierarchies, and many behaviors are due to pack life. Each pack has an alpha male and an alpha female; the alpha male is dominant over all other members of the pack and the alpha female is second highest.
Despite popular belief, the hierarchy isn't a constant struggle maintained through acts of aggression; many wolves -- and dogs -- naturally follow a leader, and the leaders may show dominant acts such as mounting without thoroughly being aggressive. Marking territory, vocalizing, moving food to a certain area and guarding the home or family are all behaviors the domestic dog has retained from the wolf's natural instinct to protect, feed and serve the pack.
Many of your dog's annoying habits are innate behaviors passed down through generations from wolf ancestors. Digging, barking, howling, marking, mounting and resource guarding are habits that may annoy you, but to your dog, these behaviors are a necessary part of life. Vocalizing in the form of barks, howls or other sounds, for example, is used in wolf packs to alert the pack of danger, a kill or intruders, or to give the barker's location. Your dog barks to intimidate intruders or perceived threats, or to warn you of potential danger. Digging is an innate behavior wolves use to find prey or to make recessed dirt "beds" to protect them from heat or other elements.
When the wolf began living closer with humans, the domestication process was mutually beneficial. Man quickly learned that wolves could hunt well and collaboratively; wolves were able to feed on scraps and carcasses left by man. Over the years of developing different breeds, certain instincts were deliberately encouraged. For example, a herding breed's instinct comes from its prey drive; a retriever's willingness to bring back game is based on the instinct to bring food back to the pack; and a guard dog's instincts drive him to protect his territory and pack.
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