A commentary on the history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

The ebb and flow of human migration across the planet can nowadays be probed with advanced archaeology, linguistics, anthropology and genomics. Together, these can provide a convincing picture of the various divergences and convergences of different human populations across vast areas. It is now possible to better understand how, why and where a particular group or society arose. Professor Naruya Saitou of the Population Genetics Laboratory at the National Institute of Genetics in Mishima has dedicated his career to the synthesis of these disciplines. The current focus of his research is on understanding the origins and formation of the Yaponesian people. This broad term was coined by writer Toshio Shimao in 1960s to encompass the diverse peoples of the Japanese Archipelago over its many thousands of years of inhabitation. Saitou's research is helping to uncover Japan's ancient past.

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Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people

Journal of Human Genetics ◽

10.1038/s10038-020-00898-3 ◽

2021 ◽

Author(s):

Timothy Jinam ◽

Yosuke Kawai ◽

Yoichiro Kamatani ◽

Shunro Sonoda ◽

Kanro Makisumi ◽

...

Keyword(s):

Phylogenetic Network ◽

Principal Component ◽

Human Populations ◽

Structure Model ◽

Rice Farming ◽

Asian Continent ◽

Dual Structure ◽

Snp Data ◽

Genome Wide ◽

Kagoshima Prefecture

AbstractThe “Dual Structure” model on the formation of the modern Japanese population assumes that the indigenous hunter-gathering population (symbolized as Jomon people) admixed with rice-farming population (symbolized as Yayoi people) who migrated from the Asian continent after the Yayoi period started. The Jomon component remained high both in Ainu and Okinawa people who mainly reside in northern and southern Japan, respectively, while the Yayoi component is higher in the mainland Japanese (Yamato people). The model has been well supported by genetic data, but the Yamato population was mostly represented by people from Tokyo area. We generated new genome-wide SNP data using Japonica Array for 45 individuals in Izumo City of Shimane Prefecture and for 72 individuals in Makurazaki City of Kagoshima Prefecture in Southern Kyushu, and compared these data with those of other human populations in East Asia, including BioBank Japan data. Using principal component analysis, phylogenetic network, and f4 tests, we found that Izumo, Makurazaki, and Tohoku populations are slightly differentiated from Kanto (including Tokyo), Tokai, and Kinki regions. These results suggest the substructure within Mainland Japanese maybe caused by multiple migration events from the Asian continent following the Jomon period, and we propose a modified version of “Dual Structure” model called the “Inner-Dual Structure” model.

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Reassessing the concept of the ‘Neolithic’ in the Jomon of Western Japan

Documenta Praehistorica ◽

10.4312/dp.34.1 ◽

2007 ◽

Vol 34 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Simon Kaner ◽

Takeshi Ishikawa

Keyword(s):

Large Scale ◽

Population Densities ◽

Neolithic Transition ◽

Japanese Archipelago ◽

History Of ◽

Western Japan ◽

The Japanese Archipelago ◽

Lower Population ◽

Late Palaeolithic

The concept of the Mesolithic/Neolithic transition is difficult to apply in the Japanese archipelago. The earliest pottery usage occurs in late Palaeolithic contexts. Holocene foragers lived in stable, permanent village settlements and constructed large scale monuments, and the first real ‘agriculture’ arrived as part of a cultural package which also included metallurgy. This paper will examine the use of the term ‘Neolithic’ in the history of Japanese archaeology, with particular emphasis on what happened in the western part of the archipelago in the latter part of the Jomon period (c. 5000 BC – c. 500 BC). Recent investigations in Kyushu and Western Honshu are leading to a re-assessment of the nature of Jomon culture and society in this region, traditionally considered to have ‘lagged behind’ the more developed societies of the eastern part of the archipelago, expressed in part through much lower population densities.

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Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

Journal of Heredity ◽

10.1093/jhered/esz032 ◽

2019 ◽

Cited By ~ 1

Author(s):

Haige Han ◽

Kenneth Bryan ◽

Wunierfu Shiraigol ◽

Dongyi Bai ◽

Yiping Zhao ◽

...

Keyword(s):

Sequence Data ◽

Genomic Diversity ◽

Data Sets ◽

Domestic Horse ◽

Snp Data ◽

Genome Wide ◽

History Of ◽

Genomic Characterization ◽

Mongolian Horse ◽

Free Ranging

Abstract The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

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Radiation history of Asian Asarum (sect. Heterotropa, Aristolochiaceae) resolved using a phylogenomic approach based on double-digested RAD-seq data

Annals of Botany ◽

10.1093/aob/mcaa072 ◽

2020 ◽

Vol 126 (2) ◽

pp. 245-260

Author(s):

Yudai Okuyama ◽

Nana Goto ◽

Atsushi J Nagano ◽

Masaki Yasugi ◽

Goro Kokubugata ◽

...

Keyword(s):

Sanger Sequencing ◽

Strong Support ◽

Phylogenomic Analysis ◽

Plant Materials ◽

Japanese Archipelago ◽

Biogeographic History ◽

Radiation History ◽

History Of ◽

The Japanese Archipelago ◽

Phylogenomic Analyses

Abstract Background and Aims The genus Asarum sect. Heterotropa (Aristolochiaceae) probably experienced rapid diversification into 62 species centred on the Japanese Archipelago and Taiwan, providing an ideal model for studying island adaptive radiation. However, resolving the phylogeny of this plant group using Sanger sequencing-based approaches has been challenging. To uncover the radiation history of Heterotropa, we employed a phylogenomic approach using double-digested RAD-seq (ddRAD-seq) to yield a sufficient number of phylogenetic signals and compared its utility with that of the Sanger sequencing-based approach. Methods We first compared the performance of phylogenetic analysis based on the plastid matK and trnL–F regions and nuclear ribosomal internal transcribed spacer (nrITS), and phylogenomic analysis based on ddRAD-seq using a reduced set of the plant materials (83 plant accessions consisting of 50 species, one subspecies and six varieties). We also conducted more thorough phylogenomic analyses including the reconstruction of biogeographic history using comprehensive samples of 135 plant accessions consisting of 54 species, one subspecies, nine varieties of Heterotropa and six outgroup species. Key Results Phylogenomic analyses of Heterotropa based on ddRAD-seq were superior to Sanger sequencing-based approaches and resulted in a fully resolved phylogenetic tree with strong support for 72.0–84.8 % (depending on the tree reconstruction methods) of the branches. We clarified the history of Heterotropa radiation and found that A. forbesii, the only deciduous Heterotropa species native to mainland China, is sister to the evergreen species (core Heterotropa) mostly distributed across the Japanese Archipelago and Taiwan. Conclusions The core Heterotropa group was divided into nine subclades, each of which had a narrow geographic distribution. Moreover, most estimated dispersal events (22 out of 24) were between adjacent areas, indicating that the range expansion has been geographically restricted throughout the radiation history. The findings enhance our understanding of the remarkable diversification of plant lineages in the Japanese Archipelago and Taiwan.

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Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

Scientific Reports ◽

10.1038/s41598-021-91357-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Fuzuki Mizuno ◽

Jun Gojobori ◽

Masahiko Kumagai ◽

Hisao Baba ◽

Yasuhiro Taniguchi ◽

...

Keyword(s):

Mitochondrial Genome ◽

Demographic History ◽

Complete Mitochondrial Genome ◽

Cultural Transition ◽

Rice Agriculture ◽

Japanese Archipelago ◽

Mitogenome Sequence ◽

Basal Group ◽

History Of ◽

The Japanese Archipelago

AbstractThe Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

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Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago

10.1101/440529 ◽

2018 ◽

Author(s):

Maribet Gamboa ◽

David Muranyi ◽

Shota Kanmori ◽

Kozo Watanabe

Keyword(s):

North America ◽

Nuclear Dna ◽

Mainland China ◽

Species Diversification ◽

Japanese Archipelago ◽

Late Neogene ◽

History Of ◽

Local Species ◽

Western Japan ◽

The Japanese Archipelago

AbstractThe generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura, Protonemura, Amphinemura and Nemoura in Japan, China, South Korea and North America. We estimated their divergence times—based on three molecular clock node calibrations—using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades—that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.

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