Six papers published on March 31, 2021 in “Anthropological Science” special issue on Yaponesian Genome Project

Press Release

0 (preface).

Preface to the special issue on the Yaponesia Genome Project

Naruya Saitou


1 (original article).

Modern human DNA analyses with special reference to the Inner-Dual structure model of Yaponesian

Timothy Jinam, Yosuke Kawai, and Naruya Saitou


2 (original article).

Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago

Noboru Adachi, Hideaki Kanzawa-Kiriyama, Nara T., Kakuda T., Nishida I., and Ken-ichi Shinoda


3 (original article).

The time-dependent evolutionary rate of mitochondrial DNA in small mammals inferred from biogeographic calibration points with reference to the late Quaternary environmental changes

Hitoshi Suzuki


4 (original article).

Geographical distribution of certain toponyms in the Samguk Sagi

Mitsuaki Endo


5 (review article).

Exploring models of human migration to the Japanese archipelago using genome-wide genetic data

Naoki Osada and Yosuke Kawai


6 (review article).

Paleogenomics of human remains in East Asia and Yaponesia focusing on current advances and future directions

Kae Koganebuchi and Hiroki Oota


Abstract of Paper 1:
Previous studies suggested two major migration events during the Jomon and Yayoi periods that affected the genetic diversity of modern Japanese (Yaponesians). We explored the possibility of a three-wave migration model by examining three datasets of modern human DNA: (1) whole mitochondrial (mt) DNA genomes of 1642 Yaponesians; (2) mtDNA haplogroup frequencies of 59105 Yaponesians from 47 prefectures; and (3) genome-wide SNP data of two Yaponesians (Ainu, Okinawa) and whole-genome sequence data of Yamato individuals, the Funadomari Jomon F23 individual, and three East Asian populations (Korean, northern Chinese, and southern Chinese). Past population size change was estimated based on dataset 1, and we clearly observed a steep population increase after the Yayoi period. Principal-component analysis and phylogenetic network analysis were applied to dataset 2, and we confirmed the pattern consistent with our model. An admixture program was used on dataset 3, and we found that the two- and three-layer migration models are both compatible with these SNP data. Taken together, these three datasets provide support for our three-wave, ‘inner dual-structure’ model.

Abstract of Paper 2:
Starting 16000 years ago, the Neolithic lifestyle known as the Jomon culture spread across the Japanese archipelago. Although extensively studied by archaeology and physical anthropology, little is known about the genetic characteristics of the Jomon people. Here, we report the entire mitogenome and partial nuclear genome of skeletal remains from the initial Jomon period that were excavated from the Higashimyo shell midden site at Saga City, Kyushu Island, Japan. This is the first genome analysis of the initial Jomon people of Kyushu Island. These results provide important data for understanding the temporal transition and regional differences of the Jomon people. The mitochondrial DNA and Y-chromosome haplogroups were similar to those found in the previously reported later Jomon people. Moreover, comparison of three nuclear genomes from the initial to final Jomon periods indicated genetic continuity throughout the Jomon period within the Japanese archipelago with no significant evidence of admixture. This indicates that the genetic differentiation found among the Jomon people was promoted by the progression of regionalization throughout the Jomon period. Further accumulation of high-quality Jomon genome data spanning a wide range of regions and ages will clarify both intimate regional and temporal differences of the Jomon people and details of their admixture history with rice farmers, as suggested by Jomon mitochondrial genome data. The results obtained from this study provide important information for further analysis.

Abstract of Paper 3:
Mitochondrial DNA (mtDNA) sequences have long been the most popular marker for assessing phylogenetic relationships and uncovering population dynamics. However, the mechanism of the nucleotide substitution rate of mtDNA remains unclear. While the evolutionary rate over tens of thousands of years is thought to be time dependent, the overall picture is not fully understood. This article presents recent achievements related to the time-dependent evolutionary rate of mtDNA in small rodents in the Japanese archipelago. The method focuses on rapid expansion events during the late Quaternary, during which there was a prolonged severe cold period and repeated abrupt warm periods, providing multiple calibration points. The global sea level fluctuation and migration to islands help to specify the calibration points. For calibration points at 11000, 15000, 53000, and 130000 years ago, the evolutionary rates were approximately 0.11, 0.11, 0.047, and 0.029 substitutions/site/million years, respectively, in the mitochondrial cytochrome b gene (Cytb). Applying the higher rate to assess the evolutionary history of the commensal house mouse (Mus musculus) and complete mitochondrial genome sequences (~16000 bp) allowed us to trace prehistoric human culture development based on millet and rice agriculture. The pattern of time-dependent evolutionary rates presented here is likely applicable to other small rodents. The Japanese archipelago is ideal for assessing evolutionary rates with biogeographic calibration points in the late Quaternary in species with multiple genetically distinct local populations.

Abstract of Paper 4:
Kim Busik’s Samguk Sagi 三国史記, History of the Three Kingdoms, dating from 1145 A.D., is renowned for including Japanese toponyms in the Korean peninsula and the north of Yalujiang district (modern Liaoning and Jilin Provinces). Kim’s work recorded the older, archaic toponyms before they were converted into sinicized (i.e. expressed with Chinese words) place names with two Chinese characters in 757 A.D. by the order of King Kyeongdeok. This paper maps specific words included in the place names of 783 locations for which the corresponding present places are evident. The following were words examined: (1) ‘river’ and its related words; (2) ‘valley’; (3) ‘mountain’ and ‘ridge’; and (4) ‘city’ and ‘burg’. Japonic-sourced toponyms are typically distributed in the central and northern areas of the Yalu River, primarily in the district of Koguryŏ; however, they go beyond these regions. The use of Chinese loanwords is noted in the southern area, where determining which language was spoken is difficult. In a town near Seoul, the stem of the toponym belongs to the Korean language, whereas the unit word belongs to the Japonic language. This usage may be attributed to bilingualism, whereby Korean-speaking inhabitants used their own language for the stem of the place name. Mongolic and/or Tungusic loanwords are also found. In some cases, determining the language origin of the current toponyms is difficult. Therefore, the minute geographical distribution of the origin languages is displayed word by word. These toponyms reflect the traces of indigenous languages and reveal that Japonic-speaking people still dwelled in the central area of the peninsula and in the northern area of the Yalu River at that period.

Abstract of Paper 5:
The origins of people in the Japanese archipelago are of long-standing interest among anthropologists, archeologists, linguists, and historians studying the history of Japan. While the ‘dual-structure’ model proposed by Hanihara in 1991 has been considered the primary working hypothesis for three decades, recent advances in DNA typing and sequencing technologies provide an unprecedented amount of present-day and ancient human nuclear genome data, which enable us to refine or extend the dual-structure model. In this review, we summarize recent genome sequencing efforts of present-day and ancient people in Asia, mostly focusing on East Asia, and we discuss the possible migration routes and admixture patterns of Japanese ancestors. We also report on a meta-analysis we performed by compiling publicly available datasets to clarify the genetic relationships of present-day and ancient Japanese populations with surrounding populations. Because the ancient genetic data from the Japanese archipelago have not yet been fully analyzed, we have to corroborate models of prehistoric human movement using not only new genetic data but also linguistic and archeological data to reconstruct a more comprehensive history of the Japanese people.

Abstract of Paper 6:
Ancient DNA analysis became paleogenomics once high-throughput sequencing technology was applied to ancient DNA sequencing. Paleogenomics based on whole-genome information from Neanderthals and Denisovans showed that small fragments of these genomes remain in the modern human genome, and corresponding studies of anatomical modern humans clarified the history of migration and expansion among Homo sapiens. Due to geographical and environmental conditions, paleogenomic studies have fallen behind in Eastern compared with Western Eurasia. Recently, however, various capture sequencing techniques, which can enrich ancient DNA, have been used in East Eurasia, and the field of paleogenomics has been further developed. This review briefly introduces the history of ancient DNA analysis leading to paleogenomics, outlines three sequencing stages (partial, draft, and complete genome sequencing) and capture methods, and discusses the necessity of high-quality sequencing for paleogenomes of Eastern Eurasia.

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