For those interested in the paleoanthropology, ethnohistory of Japan, I've found an informative little page on the subject:

Source:
http://www.republicanchina.org/Japanese.html
There are profiles of the other east asian nationalities as well. The website is written by a Chinese historian, and I believe it is accurate enough for general, casual purposes.


Layers Of Japanese Compositions

The composition of today's Japanese, like many other peoples, is quite complicated. Though today's Japanese would usually divide themselves into two groups, northerners and southerners, the actual ingredients are much more diversified than that. We could probably list at least the following subgroups:
  • Melanesian - a group of early hunters in Japan during the so-called middle Jomon period, about 10,000 years ago. Those peoples had remained stone-aged people throughout. The name Jomon comes from the archaeological artifacts from this period, mysterious clay figurines that appear to be female and clay pots used for cooking and storing food. Jomon, namely, "cord pattern", will be used for those excavations. Beginning around c. 2,500 BC and continuing for nearly a millennium, the Jomon culture spread from the Kanto Plain near modern Tokyo to the surrounding mountains.
  • Rice Culture People living on the western coast of Japan who might had migrated here from the Yangtze River Delta of China. This group of people would include Queen Himiko of Wa State referred to in Chinese history around the 2-3rd centuries. The Wa people were recorded to have tattoos over their body, in a similar fashion to the Zhejiang people in Yantze delta where the descendants of King Shaokang of Xia Dynasty (21-16th c. BC) had lived. Chen Shou's "San Guo Zhi" also recorded that the Japanese, calling themselves by the title of 'Da Fu', claimed to be descendants of 'Tai Bo' [the brother of early Zhou Dynasty ruler]. The ancient Japanese, however, did not claim heritage from Xia King Shaokang, two dynasties ahead of Zhou royal house. Japanese, whom history chronicles repeatedly likened to the tattoo natives of the Yangtze Delta, had an interesting name for one of their four islands, i.e., Kyushu, a name that literally means the "nine prefectures", which conincides with Xia Dynasty Overlord Yu's nine cauldrons.

    Recent DNA tests of the charcoal remains of rice from 2200 years ago proved that the early rice shared the same origin as that in China's Yantze Delta, while today's Japanese rice is mainly transplanted from Korea. DNA studies conducted on human remains excavated in Shandong Peninsula ( http://www.journals.uchicago.edu/AJH...34/980634.html ) suggested southern and northern points of origin for Jomon and Yayoi Japanese. On basis of various historical records and modern technology analysis, I would speculate i) that early Japanese, like early Korean, were very much connected with eastern China as a result of nascent human migration from south to north and ii) that Tungusic invasions from Manchuria gradually overtook the early Continental traits in both Korea and Japan. (My speculation is that ancient Wa Japanese with Tai Bo lineage had been wiped out or assimilated into the later immigrants from Korea. An Zhimin, at carleton.ca/~bgordon/Rice/papers/zhimin84.htm, wrote about "EFFECT OF PREHISTORIC CULTURES OF THE LOWER YANGTZE RIVER ON ANCIENT JAPAN", with speculation about pre-Han-Dynasty contacts between Japan and China.)
  • Yayoi - Mostly of Tungustic and Korean origins. They had a long history of migrations into Japan and recorded incidents of their voyages would last from 2-3 century BC to 2-3 century AD. The migrations have to do with the chain reactions on the continent, namely, the demise of the Chinese Qin Dynasty and the establishment of Han Dynasty around 206 BC. In the korean section, we mentioned Wei Man's usurpation of Old Choson and consequent relocation of Choson King to southern Korea. Some of the Koreans had been pushed off the peninsula in between, and the island of Kyushu and islands in the Tsushima Strait were already the back waters of the fishermen on two sides from very old times on.

    Tombs dating to 200-300 AD contained bronze utensils which were mainly brought over from Korea. There was a report saying that a tomb which was opened through a lightening in AD 1872 showed the dead king or emperor (Nintoku) wearing Korean clothes and the bronze utensils dated around 4th century. This wave of migration, beginning around c. 200 BC and continuing for the next hundreds of years, gradually spreaded eastward to the Kanto Plain. Based on the fact that remnants of settlements were first discovered in the Yayoi District in Tokyo, these immigrants are referred to as the Yayoi people. They brought along advanced culture that bore the marks of China's Qin/Han culture. The three major symbols of the Japanese, i.e., bronze mirror, sword, and royal seal, are exactly the same as symbols used by the Qin Dynasty.
  • Paekche Colonialists & Refugees - http://www.koreanhistoryproject.com cited a Korean saying that in 369 AD, Prince Homuda, a Paekche prince, led a expeditionary force to Japan. He landed on the northern shore of Kyushu at Hakata Bay, on the westernmost of Japan's Kyushu, and pushed his way to the agricultural plain formed by the Yodo and Yamato Rivers at the head of Osaka Bay where the Yamato Kingdom was founded.

    Japan-Korea link is most evident in the history of Korea's three kingdoms and China's participation. Tang General Su Dingfang, who had just defeated the Western Turkic Khanate in Central Asia in AD 662-666, crossed the see from Chengshan to campaign in Korea. At the request of Silla king, China came to Korea and aided Shilla in defeating both Paekche & Japanese (whose 400 warships were burnt by General Liu Rengui). The Japanese link showed the historical links between Paekche and Japan. It was the Paekche who went to Japan to pick up one of their princes and put him on the throne for sake of continuing the war efforts with Silla/Tang. After Paekche was exterminated, some remnants of the Paekche kingdom fled to Japan, and the newly arrived Koreans would be responsible for compiling Japan's history books.
  • Micronesian - Southeast Asian peoples, like Malays, who had spread across the Pacific islands, Taiwan, Ryukyu and Japan. Due to their height, they might have played a role in Chinese calling Japan 'Wa' which means people low in height literally. Chinese history recorded a name 'pygmy state' or 'dwarf state' south of Queen Himiko's Wa State in 3rd century AD. (Also possible would that the original low-height Japanese could have something to do with pigmy people from Africa, and on Chinese continent, pigmy people were caught by Wu Dynasty of Three Kingdoms era around the Huai-shui River.)
  • Ainu - Said to be a group of the aborigines of Japan. They had a religion of a bear cult which is about sacrificing a bear at an annual winter feast. Owning to migrations of people from the continent, they had been retreating to the northern islands of Japan, Sakhalin and the Kuril Islands. Today, they reside mainly on Hokkaido. Except for possibly body hair, intermarriage has led to no particular difference between them and ordinary Japanese. According to China's historical accounts, the Japanese claimed that on their island there were a group of people called 'Mao Ren', namely, hairy people (related to the Ainus?). In AD 478, Wa King sent an emissary to Liu Song Emperor Shundi, claiming that they had campaigned against 55 eastern statelets of hairy people, corroborating the fact that Yamato Japanese had just started colonizing the whole Japan islands around that timeframe and pushing against the poor hairy people.

    On basis of DNA analysis, as shown at http://www.pitt.edu/~annj/courses/notes/jomon_genes.html & http://hgm2002.hgu.mrc.ac.uk/Abstracts/Publish/WorkshopPosters/WorkshopPoster11/hgm0584.htm, Jomon could be ancestors of the Ainu people, and Jomon could be related to the Tibetans.

    http://www.boondocksnet.com/expos/wfe_1904_book26.html (by Marshall Everett ) stated that Ainu chieftan had attended the Anthropology Exhibits at the 1904 World's Fair in St Louise, with such close examinations as follow: "They [Ainu} are dark-skinned, and slow-witted, and their old men, with their long beards, look like patriarchs. They are almost the same height as the Japanese, but are heavier, and they haven't the almond eye... The Ainu have wavy hair, often curly. Black is the predominant color. The hair of the children is lighter, and often auburn. All Ainu hair is coarse and strong... They are light reddish-brown in color, and have none of the sallow yellowness of the Mongolian. They have expressive eyes, and almost every Ainu's eyes are light brown in color. Black eyes are rare among them... Their foreheads are narrow, and slope gently backward. Their noses are slightly hooked, flat and broad, with wide nostrils. They have large mouths and firm, thick lips. They have exceptionally long ear lobes."