Phylogenetic affiliation of ancient and contemporary humans inferred from mitochondrial DNA

Abstract

Nucleotide sequence analysis of the major non-coding region of human mitochondrial DNA (mtDNA) from three major races was extended with data from 27 contemporary Mongoloids (20 from southeast Asia, seven from America) and 11 Ancient Japanese bones (five from Jomon Age; 3000—6000 years b p , six from the early modern Ainu; 200-300 years BP). In both cases, the sequence was determined directly from the polymerase chain reaction products. Based on a comparison of the 482 base pair sequences from a total of 128 contemporary humans, the nucleotide diversity is estimated to be 1.46%, which is three times higher than the corresponding value estimated from restriction-enzyme analysis of the whole mtDNA genome. The phylogenetic tree revealed that all lineages are classified into at least five clusters designated as Cl — C5. Cl consists exclusively of Africans, and most Asians and Europeans formed C2, C3, C5 and C4, respectively. Phylogenetic analysis also indicated that part of the Asians, including the Japanese, subsequently diverged from the majority of Africans, and that Asians can therefore be separated into two distinct groups. Native Americans, however, appeared only in C3 and C5, suggesting that the size of the founder population was not so large during the peopling of America. Nucleotide sequences derived from ancient bones in a highly polymorphic region were also compared with those of contemporary humans. The nucleotide diversity among the 139 sequences in the region was estimated to be 2.26%. A group of ancient Japanese, including both Jomon peoples and the Ainu, showed a close phylogenetic affiliation with one group of contemporary Japanese and southeast Asians. Moreover, all of the ancient Japanese were clearly placed in a larger cluster, indicating their genealogical difference from another group of contemporary Japanese. This observation supports the immigration theory, which postulates that immigrants from the Asian continent made a considerable contribution to the formation of modern Japanese. Finally, the presence of an Asian-specific deletion was examined by using polymerase chain reaction analysis of native American samples. The deletion was found in one mummy sample. This, together with the present sequence analysis and published information, clearly shows that the Circum-Pacifican populations (Asians, Oceanians and native Americans) can be separated into two distinct mitochondrial lineages.