We have mainly 4 theories about Jomon Jin and Yayoi jin.
Recentry many people support (4).(Some deny (4).)

(1)Native Japanese (Jomon jin) were thrown out of Japan by Yayoi jin.
(2)Native Japanese (Jomon jin) were mixed with Yayoi Jin.
(3)Native Japanese gradually changed their physical features.
And they became Yayoi Jin.
(4)There lived Native Japanese.They were called Jomon Jin who had physical features from south ward.In Yayoi period,people who had physical features from nothern ward (Yayoi Jin) came to nothern Kyusyu from Eurasia.They went down to Kyusyu and up to Honsyu.Jomon Jin moved to Okinawa and Hokkaido.

According to a study of gene (blood), there are two Mongorians.
Nothern Mongorians are Japanese or Native Americans.
(Japanese or Native Americans are "Old" Mongorians.Inuit are "New" Mongorians.)
Southern Mongorians are Chinese,Filipinos,Malayans.
Tamil in India are mixed.
The origin of gene (blood) of Japanese was from near the Lake Bikal, one of a gene hunter,Matsumoto Hideo said.
DNA of Jomon people were mainly (90%) the same as DNA of people who lived near the Lake Bikal.

I got these informations from some books.
Old Mongorians have wet ear wax,and New Mongorians have dry one.
Interesting!