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I found this about.com resource page that lists tons of resources for finding your Japanese roots. From family registrys to Imperial Family tree searches, you should be able to effectively trace your roots through history through the sites give here.
https://genealogy.about.com/cs/japan/
Ancient DNA rewrites early Japanese history -- modern day populations have tripartite genetic origin. Researchers have extracted Ancient DNA from human bones to re-write early Japanese history by underlining that modern day populations in Japan have a tripartite genetic origin -- a finding that refines previously accepted views of a dual genomic ancestry. Source 6m.