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Sata H, Shimizu M, Iwasaki T, Ikeda H, Soejima A, Kozhevnikov AE, Kozhevnikova ZV, Im HT, Jang SK, Azuma T, Nagano AJ, Fujii N. Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data. JOURNAL OF PLANT RESEARCH 2021; 134:1181-1198. [PMID: 34595677 DOI: 10.1007/s10265-01339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 05/23/2023]
Abstract
To elucidate the origin and migration history of the "Mansen elements," a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000 years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further post-glacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.
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Affiliation(s)
- Haruna Sata
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Midori Shimizu
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Takaya Iwasaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Akiko Soejima
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Andrey E Kozhevnikov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Zoya V Kozhevnikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Hyoung-Tak Im
- Department of Biological Science, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Kil Jang
- East Coast Research Institute of Life Science, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung city, Gangwon-do, 25457, South Korea
| | - Takayuki Azuma
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, N3W8, Chuo-ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Noriyuki Fujii
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
- Course of Biological Science, Faculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
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Sata H, Shimizu M, Iwasaki T, Ikeda H, Soejima A, Kozhevnikov AE, Kozhevnikova ZV, Im HT, Jang SK, Azuma T, Nagano AJ, Fujii N. Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data. JOURNAL OF PLANT RESEARCH 2021; 134:1181-1198. [PMID: 34595677 DOI: 10.1007/s10265-021-01339-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
To elucidate the origin and migration history of the "Mansen elements," a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000 years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further post-glacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.
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Affiliation(s)
- Haruna Sata
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Midori Shimizu
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Takaya Iwasaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Akiko Soejima
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Andrey E Kozhevnikov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Zoya V Kozhevnikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Hyoung-Tak Im
- Department of Biological Science, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Kil Jang
- East Coast Research Institute of Life Science, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung city, Gangwon-do, 25457, South Korea
| | - Takayuki Azuma
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, N3W8, Chuo-ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Noriyuki Fujii
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
- Course of Biological Science, Faculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
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Ikeda H, Eidesen PB, Yakubov V, Barkalov V, Brochmann C, Setoguchi H. Late Pleistocene origin of the entire circumarctic range of the arctic-alpine plant Kalmia procumbens. Mol Ecol 2017; 26:5773-5783. [PMID: 28815785 DOI: 10.1111/mec.14325] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 08/06/2017] [Accepted: 08/08/2017] [Indexed: 01/18/2023]
Abstract
The circumarctic ranges of arctic-alpine plants are thought to have been established in the late Pliocene/early Pleistocene, when the modern arctic tundra was formed in response to climate cooling. Previous findings of range-wide genetic structure in arctic-alpine plants have been thought to support this hypothesis, but few studies have explicitly addressed the temporal framework of the genetic structure. Here, we estimated the demographic history of the genetic structure in the circumarctic Kalmia procumbens using sequences of multiple nuclear loci and examined whether its genetic structure reflects prolonged isolation throughout the Pleistocene. Both Bayesian clustering and phylogenetic analyses revealed genetic distinction between alpine and arctic regions, whereas detailed groupings were somewhat discordant between the analyses. By assuming a population grouping based on the phylogenetic analyses, which likely reflects a deeper intraspecific divergence, we conducted model-based analyses and demonstrated that the intraspecific genetic divergence in K. procumbens likely originated during the last glacial period. Thus, there is no need to postulate range separation throughout the Pleistocene to explain the current genetic structure in this species. This study demonstrates that range-wide genetic structure in arctic-alpine plants does not necessarily result from the late Pliocene/early Pleistocene origin of their circumarctic ranges and emphasizes the importance of a temporal framework of the current genetic structure for understanding the biogeographic history of the arctic flora.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | | | - Valentin Yakubov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Vyacheslav Barkalov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | | | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto, Japan
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