scholarly journals Population dynamics in the Japanese Archipelago since the Pleistocene

2021 ◽  
Author(s):  
Fuzuki Mizuno ◽  
Jun Gojobori ◽  
Masahiko Kumagai ◽  
Hisao Baba ◽  
Yasuhiro Taniguchi ◽  
...  
Keyword(s):  
Demographic History ◽  
Cultural Transition ◽  
Rice Agriculture ◽  
Hunter Gatherers ◽  
Japanese Archipelago ◽  
Mitogenome Sequence ◽  
History Of ◽  
Complete Mitogenome ◽  
Genetic Continuity ◽  
The Japanese Archipelago

Abstract The 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 sequence from Palaeolithic human remains. We also obtained those of Neolithic (hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome is potentially an ancestral type of haplogroup M, suggesting it is not only connected to present-day Japanese but also present-day East Asians. There were no changes in the gene pool from the hunting-gathering (Jomon) to the farming cultures (Yayoi), and this is different from in Europe, where there was no genetic continuity between hunter-gatherers and farmers. 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.

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

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.

scholarly journals Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago

2014 ◽  
Vol 31 (11) ◽  
pp. 2929-2940 ◽  
Author(s):  
Takehiro Sato ◽  
Shigeki Nakagome ◽  
Chiaki Watanabe ◽  
Kyoko Yamaguchi ◽  
Akira Kawaguchi ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
Snp Analysis ◽  
Japanese Archipelago ◽  
Genome Wide ◽  
History Of ◽  
The Japanese Archipelago

Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago

2001 ◽  
Vol 10 (6) ◽  
pp. 1357-1370 ◽  
Author(s):  
Simon J. Goodman ◽  
Hidetoshi B. Tamate ◽  
Rebecca Wilson ◽  
Junko Nagata ◽  
Shirow Tatsuzawa ◽  
...  
Keyword(s):  
Population Structure ◽  
Sika Deer ◽  
Demographic History ◽  
Cervus Nippon ◽  
Japanese Archipelago ◽  
History Of ◽  
The Japanese Archipelago

scholarly journals Effect of population structure and migration when investigating genetic continuity using ancient DNA

2016 ◽  
Author(s):  
NM Silva ◽  
S Kreutzer ◽  
C Papageorgopoulou ◽  
M Currat
Keyword(s):  
Population Structure ◽  
Ancient Dna ◽  
Isolated Populations ◽  
Hunter Gatherers ◽  
History Of ◽  
Genetic Continuity ◽  
Population Continuity ◽  
Local Hunter ◽  
And Migration ◽  
Genetic Pool

AbstractRecent advances in sequencing techniques provide means to access direct genetic snapshots from the past with ancient DNA data (aDNA) from diverse periods of human prehistory. Comparing samples taken in the same region but at different time periods may indicate if there is continuity in the peopling history of that area or if a large genetic input, such as an immigration wave, has occurred. Here we propose a new modeling approach for investigating population continuity using aDNA, including two fundamental elements in human evolution that were absent from previous methods: population structure and migration. The method also considers the extensive temporal and geographic heterogeneity commonly found in aDNA datasets. We compare our spatially-explicit approach to the previous non-spatial method and show that it is more conservative and thus suitable for testing population continuity, especially when small, isolated populations, such as prehistoric ones, are considered. Moreover, our approach also allows investigating partial population continuity and we apply it to a real dataset of ancient mitochondrial DNA. We estimate that 91% of the current genetic pool in central Europe entered the area with immigrant Neolithic farmers, but a genetic contribution of local hunter-gatherers as large as 83% cannot be entirely ruled out.

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

2007 ◽  
Vol 34 ◽  
pp. 1-7 ◽  
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.

scholarly journals Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

PLoS Genetics ◽  
2009 ◽  
Vol 5 (4) ◽  
pp. e1000448 ◽  
Author(s):  
Etienne Patin ◽  
Guillaume Laval ◽  
Luis B. Barreiro ◽  
Antonio Salas ◽  
Ornella Semino ◽  
...  
Keyword(s):  
Demographic History ◽  
Hunter Gatherers ◽  
Data Set ◽  
History Of

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

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.

Malthusian cycles among semi-sedentary Fisher-Hunter-Gatherers: The socio-economic and demographic history of Housepit 54, Bridge River site, British Columbia

2020 ◽  
Vol 59 ◽  
pp. 101181 ◽  
Author(s):  
Anna Marie Prentiss ◽  
Matthew J. Walsh ◽  
Thomas A. Foor ◽  
Kathryn Bobolinski ◽  
Ashley Hampton ◽  
...  
Keyword(s):  
British Columbia ◽  
Demographic History ◽  
Hunter Gatherers ◽  
History Of ◽  
River Site

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

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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