Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced
Abstract Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been intr...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-48079-4 |
| _version_ | 1797452749889077248 |
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| author | Ichiro Tamaki Mizuo Mizuno Tatsuo Ohtsuki Kohtaroh Shutoh Ryoichi Tabata Yoshihiro Tsunamoto Yoshihisa Suyama Yusuke Nakajima Naoki Kubo Takeru Ito Naohiko Noma Emiko Harada |
| author_facet | Ichiro Tamaki Mizuo Mizuno Tatsuo Ohtsuki Kohtaroh Shutoh Ryoichi Tabata Yoshihiro Tsunamoto Yoshihisa Suyama Yusuke Nakajima Naoki Kubo Takeru Ito Naohiko Noma Emiko Harada |
| author_sort | Ichiro Tamaki |
| collection | DOAJ |
| description | Abstract Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native. |
| first_indexed | 2024-03-09T15:13:10Z |
| format | Article |
| id | doaj.art-d852610c8f8d4b5a88d51fd6ff2e8528 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:13:10Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-d852610c8f8d4b5a88d51fd6ff2e85282023-11-26T13:17:19ZengNature PortfolioScientific Reports2045-23222023-11-0113111010.1038/s41598-023-48079-4Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introducedIchiro Tamaki0Mizuo Mizuno1Tatsuo Ohtsuki2Kohtaroh Shutoh3Ryoichi Tabata4Yoshihiro Tsunamoto5Yoshihisa Suyama6Yusuke Nakajima7Naoki Kubo8Takeru Ito9Naohiko Noma10Emiko Harada11Gifu Academy of Forest Science and CultureGifu Pharmaceutical UniversityLake Biwa MuseumThe Hokkaido University Museum, Hokkaido UniversityLake Biwa MuseumResearch Institute of Energy, Environment and Geology, Hokkaido Research OrganizationKawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku UniversitySchool of Environmental Science, The University of Shiga PrefectureSchool of Environmental Science, The University of Shiga PrefectureSchool of Environmental Science, The University of Shiga PrefectureSchool of Environmental Science, The University of Shiga PrefectureSchool of Environmental Science, The University of Shiga PrefectureAbstract Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.https://doi.org/10.1038/s41598-023-48079-4 |
| spellingShingle | Ichiro Tamaki Mizuo Mizuno Tatsuo Ohtsuki Kohtaroh Shutoh Ryoichi Tabata Yoshihiro Tsunamoto Yoshihisa Suyama Yusuke Nakajima Naoki Kubo Takeru Ito Naohiko Noma Emiko Harada Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced Scientific Reports |
| title | Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced |
| title_full | Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced |
| title_fullStr | Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced |
| title_full_unstemmed | Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced |
| title_short | Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced |
| title_sort | phylogenetic population structure and population demographic analyses reveal that vicia sepium in japan is native and not introduced |
| url | https://doi.org/10.1038/s41598-023-48079-4 |
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