The Origins of the Japanese people

The origins of the Japanese people is not entirely clear yet. It is common for Japanese people to think that Japan is not part of Asia since it is an island, cut off from the continent. This tells a lot about how they see themselves in relation to their neighbours. But in spite of what the Japanese may think of themselves, they do not have extraterrestrial origins, and are indeed related to several peoples in Asia.
We shall have to go back a long way through history and analyse in depth the genetics, culture and language of the archipelago and try to find out whether the Japanese are indeed unique, and in what way.
During the last Ice Age, which ended approximately 15,000 years ago, Japan was connected to the continent through several land bridges, notably one linking the Ryukyu Islands to Taiwan and Kyushu, one linking Kyushu to the Korean peninsula, and another one connecting Hokkaido to Sakhalin and the Siberian mainland. In fact, the Philippines and Indonesia were also connected to the Asian mainland. This allowed migrations from China and Austronesia towards Japan, about 35,000 years ago. These were the ancestors of the modern Ryukyuans (Okinawans), and the first inhabitants of all Japan.
The Ainu came from Siberia and settled in Hokkaido and Honshu some 15,000 years ago, just before the water levels started rising again. Nowadays the Ryukuyans, the Ainus and the Japanese are considered three ethnically separate groups. We will see why.
Genetic evidenceIt is now believed that the modern Japanese descend mostly from the interbreeding of the Jomon Era people (15,000-500 BCE), composed of the above Ice Age settlers, and a later arrival from China and/or Korea. Around 500 BCE, the Yayoi people crossed the see from Korea to Kyushu, bringing with them a brand new culture, based on wet rice cultivation and horses.
As we will see below, DNA tests have confirmed the likelihood of this hypothesis. About 54% of paternal lineages and 66% the maternal lineages have been identified as being of Sino-Korean origin.
DNA analysis of the Japanese peopleTwo kinds of DNA tests allow to trace back prehistoric ancestry. The first one is mitochondrial DNA (mtDNA), DNA found outside the cells' nucleus and inherited through the mother's line. The other is the Y-chromosome (Y-DNA), inherited exclusively from father to son (women do not have it). They are both inherited in an unaltered fashion for many generations, which allow geneticists to identify very old lineages and ancient ethnicities.