Until recent discoveries in molecular genetics, it has often been the belief that the domestic dog was descended from the wolf, because of a long prehistory where domestic dogs and the gray wolf were not all that different in outward physical characteristics. Studies have indicated that dogs are the oldest domesticated species, and likely originated even well before their first appearance in the archeological record 15,000 years ago where, the initial change to the diagnostic phenotype of domestic dogs was perhaps due in part to selection pressures associated with the transition from hunter gatherer to more sedentary lifestyles.

Recent genetic analyses have also suggested that many modern dog breeds have a much more recent origin of less than 200 years ago. Dogs clearly have behaviors, phenotypes, and diseases that are not evident in their wild progenitors. Finally, in the more recent evolution of dog breeds, limited interbreeding has imposed a remarkable genetic structure such that nearly all breeds represent distinct genetic pools that can be divided into at least four distinct genetic groupings; Asian/Ancient, Herding, Hunting, and Mastiff. Perhaps surprisingly, the German Shepherd dog is genetically closer related to the Bullmastiff, Rottweiler, Bulldog, or Boxer in the "Mastiff" category, than the Akita, Alaskan Malamute, Siberian Husky of the "Ancient" group, the Belgian Sheepdog or Belgian Tervuren of the "Herding" group, or the Border Collie and Australian Shepherd of the "Hunting" group.

The diverse genetic origin of the domestic dog has likely involved multiple gray wolf populations from breed inception that were even at later times backcrossed with wolves throughout history. There are examples not so many generations back in today's Czech bred German shepherd bloodlines, as developed from the experiments of kennel "z Pohranicni straze" in Libejovice (south Bohemia), in an effort to improve health, resistance and hardiness in their bloodlines used for military service and the patrolling of borders. This resulted in a recently developed breed, the "Czechoslovakian wolfdog", which originated from the 1955 breeding of a Carpathian wolf and German shepherd, and subsequently backcrossed again to wolves on three additional occasions within a 25 year period.

This substantial input of variation from wild ancestors has provided the raw material for phenotypic change, but unique development and genetic mechanisms may also have assisted the course of artificial selection. The natural history of some breeds has further restricted their genetic diversity over what is expected from breeding strategies alone. Significant events in the last 100 years, such as wars and economic depressions contribute to reducing the genetic diversity of breeds by producing severe bottleneck conditions such as political or geographical isolation, at times having reduced the effective breeding stock of particular breeds to only a few dogs.

Genetic testing results also clearly show a sex bias in the origin of breeds. The breeding potential for males is much larger than that for females because a female will produce one or two litters per year, while a single male could father a large number of litters. With a smaller number of males than females being involved in the formation of most breeds, this drastically differs from the breeding patterns in wild gray wolf populations where both sexes have similar contributions. Diversity is therefore reduced by the presence of popular sires, in what is often called "popular sire syndrome" or "founders effect". These dogs have physical features that make them particularly successful in the show ring and hunting or sporting events, and as a result, they may produce over a 100 litters in their lifetime. Therefore many breeds of purebred dogs today represent a limited genetic pool, with disease predispositions that derive from one or a small number of recent genetic founders.