Mitochondrial DNA analysis of Yayoi period human skeletal remains from the Doigahama site

Abstract

We analyzed the mitochondrial DNA extracted from 14 human skeletal remains from the Doigahama site in Japan to clarify the genetic structure of the Doigahama Yayoi population and the relationship between burial style and kinship among individuals. The sequence types obtained in this study were compared with those of the modern Japanese, northern Kyushu Yayoi and ancient Chinese populations. We found that the northern Kyushu Yayoi populations belonged to the groups that include most of the modern Japanese population. In contrast, most of the Doigahama Yayoi population belonged to the group that includes a small number of the modern Japanese population. These results suggest that the Doigahama Yayoi population might have contributed less to the formation of the modern Japanese population than the northern Kyushu Yayoi populations. Moreover, when we examined the kinship between individuals in the Doigahama site, we found that the vicinal burial of adult skeletons indicated a maternal kinship, although that of juvenile skeletons did not. The vicinal burial style might have been influenced by many factors, such as paternal lineages, periods and geographical regions, as well as maternal lineages. In addition, skeletons considered to be those of shamans or leaders had the same sequence types. Their crucial social roles may have been inherited through maternal lineage.

The fine-scale genetic structure and evolution of the Japanese population

“…Supporting the model, genetic similarity to Korean people was found to be higher in the Hondo people than in the Ryukyu and Ainu people (who presumably retain more Jomon ancestry components) in DNA studies of mitochondria [ 7 , 8 ], Y chromosome [ 9 – 11 ] and classic genetic markers [ 12 ] in modern people. Ancient mitochondrial DNA analysis of Jomon and Yayoi people also agree with the model [ 13 , 14 ]. Based on genome-wide SNP analysis of modern Japanese, the proportion of Jomon ancestry in the modern Japanese was estimated to be approximately 18% or 28% for the Hondo and Ryukyu people, respectively [ 15 ], and higher for the Ainu people [ 16 ].…”

MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome

“…Therefore, short regions, such as hypervariable regions (HVRs), have often been used in previous studies on ancient DNA from warm and humid geographical regions. [57][58][59] However, the mitochondrial genome coverages obtained from ancient remains vary according to their DNA preservation. Actually, some empirical sequencing data from prehistoric Southeast Asian samples have large defects in the D-loop, including the HVRs.…”

An assessment of postcranial indices, ratios, and body mass versus eco‐geographical variables of prehistoric Jomon, Yayoi agriculturalists, and Kumejima Islanders of Japan

“…The craniofacial studies indicate that the Yayoi shows similarity to the Northeast Asian groups in the Asian Continent where the climatic condition was colder than recent Japan (Brace & Seguchi, ; Dodo & Ishida, ; Hanihara, ; Nakahashi, ; Omoto & Saitou, ; Pietrusewsky, ; Seguchi et al, ). Also, studies of odontometrics, dental morphology, and genetic studies suggest that the Yayoi people migrated into Japan from China, or possibly Korea (Brace & Nagai, ; Brace et al, ; Hammer et al, ; Igawa et al, ; Oota, Saitou, Matsushita, & Ueda, ). However, our Yayoi data came from the middle Yayoi Period; therefore, we probably do not have the samples that were first generation Jomon‐Yayoi hybrids and indigenous Jomon groups who adapted Yayoi pottery and culture.…”

“…We agree with their conclusions. Yet, many researchers (Brace & Nagai, ; Brace et al, ; Hammer et al, ; Hanihara, ; Hanihara & Ishida, ; Igawa et al, ; Ishida et al, ; Kanzawa‐Kiriyama et al, ; Oota et al, ) will agree that the Yayoi agriculturalists made a significant genetic contribution to the Japanese mainland population. Finally, our postcrania results for Kumejima (observed variance = 0.6535; expected variance = 0.5837) agree with Ishida et al () [observed variance m / f = 1.0121; expected variance m / f = 0.8530].…”