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Yu Y, Lu Q, Lapirov AG, Freeland J, Xu X. Clear phylogeographical structures shed light on the origin and dispersal of the aquatic boreal plant Hippuris vulgaris. FRONTIERS IN PLANT SCIENCE 2022; 13:1046600. [PMID: 36518494 PMCID: PMC9742601 DOI: 10.3389/fpls.2022.1046600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Aquatic plants are an important ecological group in the arctic flora; however, their evolutionary histories remain largely unknown. In order to deepen our understanding of the evolution of these plants, we explored the phylogeographical structure of an aquatic boreal plant Hippuris vulgaris in a broad geographical sampling from Eurasia and North America using the chloroplast intergenic spacer psbA-trnH and seven nuclear microsatellite loci. Two closely-related species H. lanceolata and H. tetraphylla were also included because of their taxonomic controversy. Both chloroplast DNA sequences and nuclear microsatellite data revealed three genetic lineages with distinct distribution ranges. Incongruence between nuclear and chloroplast DNA lineages occurred in 14 samples from Russian Far East and Europe caused by inter-lineage hybridization. No private haplotypes or independent genetic clusters were evident in H. lanceolata or H. tetraphylla, suggesting that these two species should be considered conspecific ecotypes of H. vulgaris. Analysis using Approximate Bayesian Computation-Random Forest approach suggests that Hippuris vulgaris originated in China, followed by dispersal into Russia plus Northeast China, then successively westwards into Europe and North America, and finally into the Russian Far East from both North America and Russia plus Northeast China. This study is the first to elucidate the historical dispersal processes of a circumarctic aquatic plant across the entirety of its range.
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Affiliation(s)
- Yinjiao Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qixiang Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Alexander G. Lapirov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl, Russia
| | - Joanna Freeland
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan, China
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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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Yamamoto M, Ohtani M, Kurata K, Setoguchi H. Contrasting evolutionary processes during Quaternary climatic changes and historical orogenies: a case study of the Japanese endemic primroses Primula sect. Reinii. ANNALS OF BOTANY 2017; 120:943-954. [PMID: 29040379 PMCID: PMC5710608 DOI: 10.1093/aob/mcx108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/09/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Recent biogeographic studies have illustrated that Quaternary climatic changes and historical orogenies have driven the development of high levels of biodiversity. In this context, phylogenetic niche conservatism may play a role as a major precursor of allopatric speciation. However, the effects of niche evolution on the diversification patterns of plant species under rapid habitat changes are still unknown. Here, Primula section Reinii, one of the few primroses endemic to the Japanese Archipelago, was investigated. This study aimed to clarify the phylogenetic position and relationships of section Reinii, interpret the biogeographic and diversification patterns of this group and gain a better understanding of the role of climatic niche evolution in the Japanese endemic primroses. METHODS Dated phylogeny for Primula section Reinii is presented based on the sequences of six chloroplast genes and one nuclear gene. Biogeographic history was reconstructed using statistical dispersal-vicariance analysis. Macro-evolutionary modelling of the climatic niche was combined with biogeographic inferences. KEY RESULTS Section Reinii was shown to be monophyletic based on chloroplast and nuclear sequences. Fossil-calibrated dating analysis estimated that this section diverged from its sister taxon, sect. Cortusoides, around 1.82 million years ago, and intraspecific diversification occurred within the last million years. This time frame was characterized by Quaternary climatic oscillations and uplift of high mountains in Japan. Biogeographic inference suggested that this section originated at the northern end of the Japanese Archipelago and then dispersed southward to other islands. Models of climatic niche evolution indicated that the closely related species P. reinii and P. tosanensis have contrasting niche optima and rates of niche evolution. CONCLUSION Our results highlight that spatiotemporal heterogeneity in the Japanese islands may play a significant role in the biogeographic history of Japanese endemic primroses. Contrasting evolutionary processes found in closely related species illustrate the effects of climatic niche evolution on species' diversification patterns.
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Affiliation(s)
- Masaya Yamamoto
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo-ku, Kyoto, Japan
| | - Masato Ohtani
- Graduate School of Education, Yokohama National University, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Kaoruko Kurata
- Institute of Natural and Environmental Sciences, University of Hyogo, Hyogo, Sanda, Hyogo, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo-ku, Kyoto, 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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Ikeda H, Setoguchi H. Importance of Beringia for the divergence of two northern Pacific alpine plants, Phyllodoce aleutica and Phyllodoce glanduliflora (Ericaceae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Importance of demographic history for phylogeographic inference on the arctic-alpine plant Phyllodoce caerulea in East Asia. Heredity (Edinb) 2015; 116:232-8. [PMID: 26531250 DOI: 10.1038/hdy.2015.95] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 11/08/2022] Open
Abstract
Arctic-alpine plants have enormous ranges in the Northern Hemisphere. Phylogeographic studies have provided insights into their glacial survival as well as their postglacial colonization history. However, our understanding of the population dynamics of disjunct alpine populations in temperate regions remains limited. During Pleistocene cold periods, alpine populations of arctic-alpine species in East Asia were either connected to an ice-free Beringia refugium or they persisted with prolonged isolation after their establishment. To estimate which of these scenarios is more likely, we elucidated the genetic structure of Phyllodoce caerulea (Ericaceae) in Beringia and northern Japan, East Asia. Sequence variation in multiple nuclear loci revealed that P. caerulea can be distinguished into northern and southern groups. A demographic analysis demonstrated that the north-south divergence did not predate the last glacial period and detected introgression from Phyllodoce aleutica, relative widely distributed in East Asia, exclusively into the southern group. Therefore, although there has been genetic divergence between northern Japan and Beringia in P. caerulea, the divergence is unlikely to have resulted from their prolonged geographic separation throughout several cycles of glacial and interglacial periods. Instead, our study suggests that the introgression contributed to the genetic divergence of P. caerulea and that the range of P. caerulea was plausibly connected between northern Japan and Beringia during the last glacial period. Overall, our study not only provides a biogeographic insight into alpine populations of arctic-alpine plants in East Asia but also emphasizes the importance of careful interpretation of genetic structure for inferring phylogeographic history.
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Ikeda H, Yoneta Y, Higashi H, Eidesen PB, Barkalov V, Yakubov V, Brochmann C, Setoguchi H. Persistent history of the bird-dispersed arctic-alpine plant Vaccinium vitis-idaea L. (Ericaceae) in Japan. JOURNAL OF PLANT RESEARCH 2015; 128:437-444. [PMID: 25773306 DOI: 10.1007/s10265-015-0709-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/21/2014] [Indexed: 06/04/2023]
Abstract
Arctic-alpine plants have expanded and contracted their ranges in response to the Pleistocene climate oscillations. Today, many arctic-alpine plants have vast distributions in the circumarctic region as well as marginal, isolated occurrences in high mountains at lower latitudes. These marginal populations may represent relict, long-standing populations that have persisted for several cycles of cold and warm climate during the Pleistocene, or recent occurrences that either result from southward step-wise migration during the last glacial period or from recent long-distance dispersal. In light of these hypotheses, we investigated the biogeographic history of the marginal Japanese populations of the widespread arctic-alpine plant Vaccinium vitis-idaea (Ericaceae), which is bird-dispersed, potentially over long distances. We sequenced three nuclear loci and one plastid DNA region in 130 individuals from 65 localities covering its entire geographic range, with a focus on its marginal populations in Japan. We found a homogenous genetic pattern across its enormous range based on the loci analysed, in contrast to the geographically structured variation found in a previous study of amplified fragment length polymorphisms in this species. However, we found several unique haplotypes in the Japanese populations, excluding the possibility that these marginal populations result from recent southward migration. Thus, even though V. vitis-idaea is efficiently dispersed via berries, our study suggests that its isolated populations in Japan have persisted during several cycles of cold and warm climate during the Pleistocene.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan,
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Ikeda H, Higashi H, Yakubov V, Barkalov V, Setoguchi H. Phylogeographical study of the alpine plantCassiope lycopodioides(Ericaceae) suggests a range connection between the Japanese archipelago and Beringia during the Pleistocene. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hajime Ikeda
- Department of Botany; National Museum of Nature and Science; 4-1-1 Amakubo Tsukuba Ibaraki 305-0005 Japan
- Institute of Plant Science and Resources; Okayama University; 2-20-1 Chuo Kurashiki Okayama 710-0046 Japan
| | - Hiroyuki Higashi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho Sakyo-ku Kyoto 606-8501 Japan
| | - Valentin Yakubov
- Institute of Biology and Soil Sciences; Russian Academy of Sciences; Far East Branch Vladivostok 690022 Russia
| | - Vyacheslav Barkalov
- Institute of Biology and Soil Sciences; Russian Academy of Sciences; Far East Branch Vladivostok 690022 Russia
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies; Kyoto University; Yoshida-nihonmatsu-cho Sakyo-ku Kyoto 606-8501 Japan
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