Nothing like Japanese racism, it's normally accepted that their roots came from the despised Koreans. And heaven forbid that they would be related to the lowly Okinawans.:)
They don't like talking about the Ainu much either.
The Yayoi are much earlier and can be traced back through Korea to Chen. The Jomon are the earliest population with a high level of culture.
There are also, undoubtedly, some Polynesian roots in there since the Japanese language has Polynesian characteristics.
They are, as it were, a very mixed population! Part of what you perceive as "racism" is a conscious effort to paper over anything that suggests that they are not all Japanese, and homogeneous.