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 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 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

Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA

2013 ◽  
Vol 16 (2) ◽  
pp. 265-273 ◽  
Author(s):  
J. Zeyland ◽  
Ł. Wolko ◽  
J. Bocianowski ◽  
M. Szalata ◽  
R. Słomski ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Gradual Process ◽  
Mtdna Sequence ◽  
History Of

Abstract Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon- dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

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

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae)

Zootaxa ◽  
2019 ◽  
Vol 4550 (4) ◽  
pp. 585
Author(s):  
GAËL ALEIX-MATA ◽  
FRANCISCO J. RUIZ-RUANO ◽  
JESÚS M. PÉREZ ◽  
MATHIEU SARASA ◽  
ANTONIO SÁNCHEZ
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Tetrao Urogallus ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
Putative Origin ◽  
Fragmented Population ◽  
Galliform Bird

The Western Capercaillie (Tetrao urogallus) is a galliform bird of boreal climax forests from Scandinavia to eastern Siberia, with a fragmented population in southwestern Europe. We extracted the DNA of T. urogallus aquitanicus and obtained the complete mitochondrial genome (mitogenome) sequence by combining Illumina and Sanger sequencing sequence data. The mitochondrial genome of T. urogallus is 16,683 bp long and is very similar to that of Lyrurus tetrix (16,677 bp). The T. urogallus mitogenome contains the normal 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region. The number, order, and orientation of the mitochondrial genes are the same as in L. tetrix and in other species of the same and other bird families. The three domains of the control region contained conserved sequences (ETAS; CSBs), boxes (F, E, D, C, B, BS box), the putative origin of replication of the H-strand (OH) and bidirectional promoters of translation (LSP/HSP). 

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 The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

2020 ◽  
Author(s):  
Igor Filipović ◽  
James P. Hereward ◽  
Gordana Rašić ◽  
Gregor J. Devine ◽  
Michael J. Furlong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Invasive Pest ◽  
Long Control Region ◽  
Trna Genes ◽  
Oryctes Rhinoceros ◽  
Mitogenome Sequence ◽  
Long Read

AbstractThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitochondrial genome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.The complete circular mitochondrial genome of O. rhinoceros is 20,898 bp-long, with a gene content canonical for insects (13 PCGs, 2 rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the CRB mitogenome sequence and annotation.

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.

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