Mitochondrial genome variation in eastern Asia and the peopling of Japan.
To construct an East Asia mitochondrial DNA (mtDNA) phylogeny, we sequenced the complete mitochondrial genomes of 672 Japanese individuals (http://www.giib.or.jp/mtsnp/index_e.html). This allowed us to perform a phylogenetic analysis with a pool of 942 Asiatic sequences. New clades and subclades emerged from the Japanese data. On the basis of this unequivocal phylogeny, we classified 4713 Asian partial mitochondrial sequences, with <10% ambiguity. Applying population and phylogeographic methods, we used these sequences to shed light on the controversial issue of the peopling of Japan. Population-based comparisons confirmed that present-day Japanese have their closest genetic affinity to northern Asian populations, especially to Koreans, which finding is congruent with the proposed Continental gene flow to Japan after the Yayoi period. This phylogeographic approach unraveled a high degree of differentiation in Paleolithic Japanese. Ancient southern and northern migrations were detected based on the existence of basic M and N lineages in Ryukyuans and Ainu. Direct connections with Tibet, parallel to those found for the Y-chromosome, were also apparent. Furthermore, the highest diversity found in Japan for some derived clades suggests that Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.
Tanaka
Masashi
M
Department of Gene Therapy, Gifu International Institute of Biotechnology, Kakamigahara, Gifu 504-0838, Japan. mtanaka@giib
Cabrera
Vicente M
VM
González
Ana M
AM
Larruga
José M
JM
Takeyasu
Takeshi
T
Fuku
Noriyuki
N
Guo
Li-Jun
LJ
Hirose
Raita
R
Fujita
Yasunori
Y
Kurata
Miyuki
M
Shinoda
Ken-ichi
K
Umetsu
Kazuo
K
Yamada
Yoshiji
Y
Oshida
Yoshiharu
Y
Sato
Yuzo
Y
Hattori
Nobutaka
N
Mizuno
Yoshikuni
Y
Arai
Yasumichi
Y
Hirose
Nobuyoshi
N
Ohta
Shigeo
S
Ogawa
Osamu
O
Tanaka
Yasushi
Y
Kawamori
Ryuzo
R
Shamoto-Nagai
Masayo
M
Maruyama
Wakako
W
Shimokata
Hiroshi
H
Suzuki
Ryota
R
Shimodaira
Hidetoshi
H
D004272:DNA, Mitochondrial / Q000235:genetics*; D005202:Asia, Eastern; D015894:Genome, Human; D006801:Humans; D007564:Japan; D010802:Phylogeny
D004272:DNA, Mitochondrial