It comes down to a single dominant "retrogene." The "trait called chondrodysplasia — causing legs that are short relative to body size, curved and heavier-boned than normal."
[R]esearchers pinpointed an extra stretch of DNA on chromosome 18 in every dog from the eight short-legged breeds [95 dogs in all], but in none of 204 control dogs they examined.
Retrogenes arise when RNA erroneously puts an extra copy of a gene into a genome, in this case a gene related to limb development.
This particular trait is not found in wolves, so it probably arose "after dogs first became domesticated and before division of early dogs into modern breeds, putting the range . . . anywhere between 300 and 15,000 years ago."
The Domestication of Dogs
Dogs appear to be the first animals to be domesticated. All other domesticated animals appear to have been domesticated after the neolithic revolution, a technological revolution in human pre-history, which took place roughly contemporaneously in several separate places around the globe with the domestication of different plants and animals.
Dogs also appear to be the only domesticated animal that proto-Native Americans brought with them to the New World from Asia, again vouching for their domestication as pre-neolithic.
Australia's native dog, the Dingo, unlike most distinctive Australian fauna, is not marsupial. "Dingoes were the only big placental mammals in Australia, apart from humans." They are most closely related to the dogs found in Thailand. The breed appears to have arisen in the vicinity of Thailand, Vietnam and Indonesia about 5,000-5,500 years ago. Current theories place its arrival in Australia at 3,500 to 4,000 years ago, probably via boats from Southeast Asia that landed on Australia's North Coast. This is consistent with genetic evidence of a very small founding population for dingos, possibly a single pregnant dog. This date is also consistent with the absence of dingos from Tasmania, which separated from Australia about 12,000 years ago, after aborigine populations arrived, but before the dingos arrived on the continent. Dingos are believed to have caused the extinction of several species, including the Tasmanian devil, on mainland Australia.
Dogs were not domesticated 40,000 years ago. Dingos arrived tens of thousands of years after Australia's aborigines originally migrated to Australia, a date at least 40,000 years ago and quite probably 70,000 years ago.
Aboriginal populations were present in both mainland Australia and Tasmania when Europeans first arrived. At that time there were 315,000-750,000 or so aboriginals people living in Australia divided into 250 or more nations with separate but related languages. Old world diseases like smallpox killed about half of the aboriginal population early on in British colonization including about 90% of people in the area of first contact.
Melting glaciers caused the distance between Australia and other land masses to increase and flooded the land bridge between Australia and New Guinea around 6,000 years ago. At the time the Australia aboriginal population is believed to arrive, the trip would have involved sea intervals of a minimum of 55 miles by sea.
Pre-European Australia did not see the domestication of plants and animals, or the development of farm economies found on other continents in the neolithic revolution outside the Murray Basin, in far Southeastern Australia, where there was fish farming and hay stacks of stored grain were found.
Dark Haired Wolves
Another trait with a clear genetic identity in dogs and wolves (who can interbreed as a single species) is the gene for a black coat, which wild wolves appear to have inherited from a domesticated dog mating.
A specific mutation in a stretch of DNA called the K locus is to blame for giving some domesticated dogs black hair . . . most black labs, poodles and shepherds have this mutation. . . . researchers found that 102 of 104 black-colored [North American gray] wolves [in Yellowstone National Park] carry the same mutation in their DNA as black dogs, whereas none of 120 lighter gray-colored wolves had the mutation.
Dark fur has proven adaptive for forest wolves, while light fur is more common in wolves on the tundra.