The Jomon people kept and used dogs in hunting, and possibly as pack animals for carrying loads. We know the dogs were not eaten by the Jomon people (by examining their kitchen middens or kitchen dumping site). Dogs were probably special members of Jomon society because many dogs had proper burials(see Asahi news report at the bottom of this page). Human footprints and dog paw prints were found inside several excavated ruins of 3,000 year old Jomon pit houses in Shiga prefecture. This has scholars convinced that the Jomon people kept dogs as pets.
Studies comparing DNA of Jomon dogs and 6 breeds of Japanese native dogs show that Japanese native dogs are likely descended from the Jomon dog of prehistoric times. DNA studies also show that among the native Japanese dog breeds, the Shiba dog has the lowest genetic diversity and thus is most likely to be directly descended from ancient prehistoric breeds. Jomon dogs were smaller than today’s Shiba dog and other native breeds.
The ancestors of the Jomon dogs were likely among the earliest ancestors of modern dogs around the world. An earlier DNA study showed that humans first bred domesticated dogs sometime around 15,000 years ago in east Asia, and that that 95 percent of dogs from Africa, Asia, Europe, and Arctic regions of North America were descended from three original female ancestors in East Asia from whose offspring then spread throughout the world along with migrating humans or through trade. A more recent study confirmed the findings but elucidated that the domestication of the dog took place in southern China sometime less than 16,500 years ago. However, the latest study contradicts those findings stating that dogs were first domesticated in the Middle East, but those dogs in East Asia may have intermingled with wolves.
Another animal the Jomon might have domesticated is the wild boar. Boar remains were not found in Sado Island or Izu Island before 7,000 BC so boars were not native to the Izu islands or Sado island before this date. Because boars cannot swim, archaeologists know that the Jomon people carried the animals over to the islands in their dugouts or rafts and bred them over there.
It was traditionally believed that horses first appeared during the Kofun period, when they were introduced from Korea for riding and warfare. Recently, horse remains found in over 500 Jomon sites have undergone examination. The earliest of the horse remains, many of which were found in Jomon shellmound sites, date back to the Late Jomon period. These horses were ancestors of the present day Kiso wild horse of Japan. It is speculated that they might have been domesticated, at least by the Yayoi period, as an examination of bone fossils showed they were larger by the Yayoi period.
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MtDNA data indicates a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves, Molecular Biology and Evolution, doi:10.1093/molbev/msp19
New DNA research points to origins of dogs (World Socialist Website, 14 Jan, 2003) Excerpts: “A recent issue of the American journal Science has reported new DNA evidence indicating that humans first bred domesticated dogs approximately 15,000 years ago in east Asia.
Skulls of dogs excavated 50 years ago turn out to be 7,000 years old (Asahi Shimbun, November 18, 2012)
The skulls of two dogs found in excavations of Jomon period remains in Ehime Prefecture (Provided by Keio University)
The bond between man and man’s best friend in Japan may have begun earlier than thought.
The skulls of two dogs excavated 50 years ago and thought lost were rediscovered and confirmed to have been buried 7,000 years ago, Keio University researchers said Nov. 2.
The finding, reported at the 66th annual meeting of the Anthropological Society of Nippon, held at Keio University’s Hiyoshi campus in Yokohama, is expected to provide a clue to determining how and for how long dogs and humans have been coexisting.
Since the skulls were excavated at an archeological dig at the Kamikuroiwa Iwakage site in Mikawa (present Kumakogen), Ehime Prefecture, in 1962, the bones were suspected of coming from Japan’s oldest buried dogs, dating to the early Jomon period, which dates back to about 9,000 years ago.
The bones, however, went missing.
After rediscovering the skulls in archaeological storage at Keio University’s Mita campus in Tokyo’s Minato Ward in spring last year, the researchers, led by Takao Sato, a professional of animal archeology at Keio University, conducted a radiocarbon measurement of them. The researchers said the results showed the dogs were buried 7,200 to 7,300 years ago.
In addition, a stable isotope ratio analysis was performed to determine the diet of the ancient dogs.
The analysis found that each canine was about 40 centimeters tall, or about the size of the modern Shiba Inu breed, and likely were carnivorous.
There is a strong possibility that the canines were used as hunting dogs, the researchers said.
By NAOKI KIMURA/ Staff Write
Heritage of Japan 
Do you have any information about the original japanese horses ancestors of the present day Kiso?
From where did they come?
If they came to Japanese islands with the Yayoi people how those horses were used at the same time from the Emishi people, in wars between them?
Read the horse pages on our website. According to emerging forensic work on horses, fossil bones of horse ancestors have turned up … it is thought local species were here since Paleolithic times, but that the conditions on the archipelago are not really conducive to large populations of horses. It is know for certain that horses were imported from the continent during kofun era, and horses probably entered Japan in very small numbers probably because shipping technology was nascent and sea crossings journeys were still hazardous. It took time for the horses to multiply and for skilled people who knew how to care for the horses to be trained before they became an advantage in warfare … probably coinciding with or being a decisive factor in the unifying of the Yamato state. In any case, although local horses had been present, it is thought they were only wild or perhaps domesticated as beasts of burden. The small, stocky physique of the early horses did not make them suitable for warfare breeding purposes, for that the Yamato elite looked to continental types of horses probably of Steppe or Persian origin. DNA studies of local populations of horses in Japan at the present time confirm only the continental gene is present leading experts to speculate that local horses may even have become extinct sometime ancient Japan.
Delightful reading! However, though I don’t have a specific, scholarly reference for you, I do believe that Japanese wild boars can and do swim.