2021/11/27 更新

写真a

イケダ ハジメ
池田 啓
IKEDA Hajime
所属
資源植物科学研究所 准教授
職名
准教授

学位

  • 博士(人間・環境学) ( 2010年3月   京都大学 )

研究キーワード

  • 進化生理学

  • 周北極ー高山植物

  • 種分化

  • 高山植物

  • フィトクロム

  • 系統地理学

  • 適応進化

  • 進化生理学

研究分野

  • ライフサイエンス / 生態学、環境学

  • ライフサイエンス / 多様性生物学、分類学

学歴

  • 京都大学    

    2005年4月 - 2010年3月

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  • 京都大学    

    2002年4月 - 2005年3月

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  • 京都大学   Faculty of Agriculture  

    2001年4月 - 2002年3月

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経歴

  • 岡山大学   資源植物科学研究所   准教授

    2018年4月 - 現在

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  • 岡山大学   資源植物科学研究所   助教

    2013年4月 - 2018年3月

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  • 国立科学博物館   植物研究部   研究員

    2011年4月 - 2013年3月

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  • 東京大学   理学(系)研究科(研究院)   特任助教(gCOE)

    2011年

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所属学協会

委員歴

  • 日本植物分類学会   英文誌(APG)編集委員  

    2021年1月 - 現在   

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  • 日本植物分類学会   監事  

    2020年1月 - 現在   

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  • 日本植物分類学会   会計幹事  

    2015年1月 - 2018年12月   

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    団体区分:学協会

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  • 日本植物学会   英文誌(JPR) 編集委員会メンバー  

    2012年3月 - 現在   

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    団体区分:学協会

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  • 日本植物学会   広報委員  

    2012年1月 - 2014年12月   

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    団体区分:学協会

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論文

  • Divergence in red light responses associated with thermal reversion of phytochrome B between high- and low-latitude species. 国際誌

    Hajime Ikeda, Tomomi Suzuki, Yoshito Oka, A Lovisa S Gustafsson, Christian Brochmann, Nobuyoshi Mochizuki, Akira Nagatani

    New phytologist   231 ( 1 )   75 - 84   2021年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Phytochromes play a central role in mediating adaptive responses to light and temperature throughout plant life cycles. Despite evidence for adaptive importance of natural variation in phytochromes, little information is known about molecular mechanisms that modulate physiological responses of phytochromes in nature. We show evolutionary divergence in physiological responses relevant to thermal stability of a physiologically active form of phytochrome (Pfr) between two sister species of Brassicaceae growing at different latitudes. The higher latitude species (Cardamine bellidifolia; Cb) responded more strongly to light-limited conditions compared with its lower latitude sister (C. nipponica; Cn). Moreover, CbPHYB conferred stronger responses to both light-limited and warm conditions in the phyB-deficient mutant of Arabidopsis thaliana than CnPHYB: that is Pfr CbphyB was more stable in nuclei than CnphyB. Our findings suggest that fine tuning Pfr stability is a fundamental mechanism for plants to optimise phytochrome-related traits in their evolution and adapt to spatially varying environments, and open a new avenue to understand molecular mechanisms that fine tune phytochrome responses in nature.

    DOI: 10.1111/nph.17381

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  • East Asian origin of the widespread alpine snow-bed herb,Primula cuneifolia(Primulaceae), in the northern Pacific region

    Hajime Ikeda, Valentin Yakubov, Vyacheslav Barkalov, Kazuhiro Sato, Noriyuki Fujii

    JOURNAL OF BIOGEOGRAPHY   47 ( 10 )   2181 - 2193   2020年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY  

    Aim The evolutionary importance of southern mountain ranges has been noted for alpine as well as arctic-alpine plants. However, it remains unclear whether these isolated marginal populations of cold-adapted species have contributed to the establishment of their current widespread distribution. We aim to explore the molecular evidence for the recent northward migration of alpine snow-bed species in the northern Pacific region. Location Japanese Archipelago, Kamchatka Peninsula, Alaska. Taxon Primula cuneifoliaLedeb., the wedgeleaf primrose, distributed in high mountains across the northern Pacific region and its sister species,Primula nipponicaYatabe, which is endemic to northern Japan. Methods The phylogenetic relationships and genetic structure ofP. cuneifoliaand its sister species were estimated using multiple loci from genotyping by random amplicon sequencing-direct (GRAS-Di) analyses. The temporal framework of genetic divergence was estimated using the isolation-with-migration model. The post-glacial range shift was inferred using approximate Bayesian computation and ecological niche modelling. Results Phylogenetic analyses revealed thatP.cuneifoliadiverged into four clades, among which the southernmost clade in Japan diverged earlier than the northern clades. The Japanese clade likely diverged during the last glacial period, followed by further post-glacial divergence of clades in the Kamchatka Peninsula and Alaska. Main conclusion Our study demonstrated thatP.cuneifoliaoriginated in Japan and spread northward into the northern Pacific region during and after the last glacial period. This finding provides the first evidence suggesting that population persistence and genetic divergence as well as speciation in the less glaciated mountains in Japan play important roles in the diversity and distribution of alpine plants in the northern Pacific region.

    DOI: 10.1111/jbi.13918

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  • Post-glacial East Asian origin of the alpine shrub Phyllodoce aleutica (Ericaceae) in Beringia 査読

    Hajime Ikeda, Valentin Yakubov, Vyacheslav Barkalov, Hiroaki Setoguchi

    Journal of Biogeography   45 ( 6 )   1261 - 1274   2018年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Blackwell Publishing Ltd  

    Aim: The ice-free area around the Bering Land Bridge, Beringia, has been noted as an important refugium of organisms preferring cold environments such as arctic-alpine plants throughout the Pleistocene climate oscillations. Although numerous phylogeographical studies have supported this refugium, recent studies have challenged the idea of a homogeneous refugium in Beringia. We aim to examine a novel scenario of the post-glacial colonization history of an alpine plant Phyllodoce aleutica in Beringia. Location: The Japanese Archipelago, the Kamchatka Peninsula, the Aleutian Islands, Alaska. Method: The range-wide genetic structure of P. aleutica was elucidated by sequencing 13 nuclear loci. The phylogeographical history was inferred using model-based approaches based on coalescent simulations together with the potential distributions predicted by ecological niche modelling. Results: Bayesian clustering and phylogenetic networks revealed that P. aleutica was divided into three geographically structured groups: the main island of the Japanese Archipelago, the northern island of the archipelago (Hokkaido) and Beringia, including eastern Hokkaido. The demographic history underlying the genetic structure and the potential distributions at present and during Last Glacial Maximum suggest that their divergence likely predated the last glacial period. Except for genetic admixture with the sister species Phyllodoce glanduliflora, populations in Alaska exhibited lower genetic diversity than those in East Asia and exclusively shared two widespread genotypes. Approximate Bayesian computation showed that a demographic model postulating post-glacial expansion into Alaska fit better than alternative models. Main conclusions: Our study suggests that P. aleutica in eastern Beringia originated through post-glacial colonization from East Asia, providing novel insight into the biogeographical history of alpine flora in Beringia.

    DOI: 10.1111/jbi.13230

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  • Late Pleistocene origin of the entire circumarctic range of the arctic-alpine plant Kalmia procumbens 査読

    Hajime Ikeda, Pernille Bronken Eidesen, Valentin Yakubov, Vyacheslav Barkalov, Christian Brochmann, Hiroaki Setoguchi

    MOLECULAR ECOLOGY   26 ( 20 )   5773 - 5783   2017年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY  

    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 bio-geographic history of the arctic flora.

    DOI: 10.1111/mec.14325

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  • Phylogeographical insight into the Aleutian flora inferred from the historical range shifts of the alpine shrub Therorhodion camtschaticum (Pall.) Small (Ericaceae) 査読

    Daijiro Hata, Hiroyuki Higashi, Valentin Yakubov, Vyacheslav Barkalov, Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF BIOGEOGRAPHY   44 ( 2 )   283 - 293   2017年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    AimThe Aleutian Islands, one of the southern margins of Beringia, were covered with ice caps during the Last Glacial Maximum (LGM). Although insular refugia for animal species have been hypothesized in this region, phylogeographical studies have never explored the biogeographical history of plant species. We aim to assess the population history of the flora of the Aleutian Islands and its biogeographical relevance to East Asia.
    LocationThe Aleutian Islands, Kamchatka, the Japanese Archipelago.
    MethodsWe sequenced seven nuclear loci from the alpine shrub Therorhodion camtschaticum (Pall.) Small (Ericaceae) and elucidated the geographical distribution of genetic variation. The divergence history among populations from the Aleutian Islands, Kamchatka and northern Japan was inferred by analyses based on coalescent simulations.
    ResultsPopulations were genetically distinct between northern Japan and Beringia. In spite of the genetic differentiation, the divergence between Beringia and northern Japan occurred during or after the last glacial period [maximum-likelihood estimates (MLEs)=10.6-15.5ka with 95% highest posterior densities (HPDs): 1.7-43.5ka]. The latter region has a larger population size than the former region. In contrast, widespread genetic similarity was revealed among the geographically separated populations in the Aleutian Islands and southern Kamchatka. Among these populations, a model assuming population decline fits better than a model that assumes either constant population size or population growth.
    Main conclusionsOur study suggests that insular refugia were unlikely for T. camtschaticum in the Aleutian Islands. Instead, T. camtschaticum may have had a wider range during LGM, encompassing both the Aleutian Islands and southern Kamchatka, or have colonized the Aleutian Islands from a LGM refugium that was the source of colonization into southern Kamchatka as well or encompassed the latter region. Our study provides novel insight into the biogeographical history of terrestrial biota in the Aleutian Islands.

    DOI: 10.1111/jbi.12876

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  • Molecular evidence for ancient relicts of arctic-alpine plants in East Asia 査読

    Hajime Ikeda, Valentin Yakubov, Vyacheslav Barkalov, Hiroaki Setoguchi

    NEW PHYTOLOGIST   203 ( 3 )   980 - 988   2014年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Following climate cooling at the end of the Tertiary, arctic-alpine plants attained most of their extant species diversity. Because East Asia was not heavily glaciated, the importance of this region as a location for the long-term persistence of these species and their subsequent endemism during the Pleistocene was proposed in early discussions of phytogeography. However, this hypothesis remains to be fully tested.
    Here, we address this hypothesis by elucidating the phylogenetic history of Phyllodoce (Ericaceae).
    A phylogenetic tree based on multiple nuclear loci revealed that Phyllodoce nipponica was not derived from widespread species such as the arctic-alpine Phyllodoce caerulea, but rather represented an independent lineage sister to the clade of widespread relatives. Molecular dating indicated a mid-Pleistocene divergence of P. nipponica.
    These findings exclude the hypothesis that P. nipponica was derived from an arctic-alpine species that extended its range southwards during recent glacial periods. Instead, our results support the hypothesis that P. nipponica is an ancestral species which persisted in the Japanese archipelago during the mid-and late Pleistocene. Our findings demonstrate support for the early proposal and shed light on the importance of the Japanese archipelago for the evolution and persistence of arctic-alpine species.

    DOI: 10.1111/nph.12863

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  • Pleistocene climatic oscillations and the speciation history of an alpine endemic and a widespread arctic-alpine plant 査読

    Hajime Ikeda, Tor Carlsen, Noriyuki Fujii, Christian Brochmann, Hiroaki Setoguchi

    NEW PHYTOLOGIST   194 ( 2 )   583 - 594   2012年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Even in cases in which geographic isolation appears to have driven the speciation of regional endemics, range shifts during the Pleistocene climatic oscillations may also have influenced their evolutionary history. Elucidating speciation history can provide novel insights into evolutionary dynamics following climatic oscillations.
    We demonstrated a sister relationship between the Japanese alpine endemic Cardamine nipponica and the currently allopatric, widespread arctic-alpine Cardamine bellidifolia (Brassicaceae) based on internal transcribed spacer (ITS) sequences and 10 other nuclear genes. Speciation history was inferred using demographic parameters under the isolation with migration model.
    The estimated demographic parameters showed that the population size of C. nipponica was similar to that of C. bellidifolia and that gene flow occurred exclusively from C. nipponica to C. bellidifolia after speciation.
    The inferred speciation history, which included gene flow, suggests that geographic barriers between the peripheral C. nipponica and the widespread C. bellidifolia were reduced during the Pleistocene. The asymmetric introgression implies that genetic isolation may have been involved in the speciation of C. nipponica. Our results suggest that even currently allopatric species may not have diverged solely under geographic isolation, and that their evolutionary history may have been influenced by Pleistocene range dynamics.

    DOI: 10.1111/j.1469-8137.2012.04061.x

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  • Natural selection on PHYE by latitude in the Japanese archipelago: insight from locus specific phylogeographic structure in Arcterica nana (Ericaceae) 査読

    Hajime Ikeda, Hiroaki Setoguchi

    MOLECULAR ECOLOGY   19 ( 13 )   2779 - 2791   2010年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY  

    Phytochromes play a key role in allowing plants to monitor their surrounding environment and, conversely, adaptation to local environments has driven the evolutionary history of phytochromes. As a result of natural selection, polymorphisms in phytochrome genes would thus be expected to exhibit locus-specific phylogeographic structure. To evaluate this hypothesis, we conducted a phylogeographic investigation based on four nuclear genes, including two phytochrome genes (PHYB and PHYE) using 155 samples of Arcterica nana from the entire range of the Japanese archipelago. Bayesian clustering revealed geographic differentiation between northern and southern Japan when all four genes were included. However, this geographic differentiation is inconsistent with previously reported genetic structure of genome-wide polymorphisms based on amplified fragment length polymorphisms, as these did not show geographic differentiation throughout the Japanese archipelago. In contrast, the north-south differentiation was not apparent when PHYE was excluded. This indicates that PHYE alone could be responsible for the north-south differentiation (F-CT = 0.15, P < 0.001). Furthermore, a single nonsynonymous polymorphism (C360T) strongly contributed to geographic differentiation (F-CT = 0.57, P < 0.001) and its corresponding amino acid replacement (P120L) was significantly under positive selection based on maximum likelihood analysis (P = 0.98). Consequently, the locus-specific geographic differentiation in PHYE could be caused by natural selection, suggesting the involvement of PHYE in local adaptation between populations of A. nana in northern and southern Japan. This finding is consistent with a previous study on Cardamine nipponica, indicating the importance of PHYE for local adaptation in Japanese alpine plants.

    DOI: 10.1111/j.1365-294X.2010.04700.x

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  • Application of the Isolation with Migration Model Demonstrates the Pleistocene Origin of Geographic Differentiation in Cardamine nipponica (Brassicaceae), an Endemic Japanese Alpine Plant 査読

    Hajime Ikeda, Noriyuki Fujii, Hiroaki Setoguchi

    MOLECULAR BIOLOGY AND EVOLUTION   26 ( 10 )   2207 - 2216   2009年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    The Pleistocene was characterized by it cyclic pattern of cold and warm climatic periods, or climatic oscillations, which caused fluctuations in the distributions of organisms. This resulted in drastic changes in demography, thereby accelerating the genetic divergence of populations. Phylogeographic studies have elucidated the history of populations during the Pleistocene. However, given the lack of model-based analysis Of Population histories, previous phylogeographic studies could not adequately evaluate the effect of these Pleistocene climatic oscillations oil the genetic divergence and migration events between populations. Populations of Japanese alpine plants in central and northern Japan are highly differentiated, and a history of isolation between regions during the Pleistocene was inferred. Using sequences of 10 nuclear genes (ca. approximately 7,000 bp in total) from Cardamine nipponica (Brassicaceae), we applied all isolation with migration (IM) model to test the significance of the isolation history between central and northern Japan and to assess whether range shifts during the Pleistocene climatic oscillations were involved in the genetic differentiation between regions. The estimated divergence time indicates that the two regions were separated about 100,000-110,000 years ago. The exclusive occurrence of closely related haplotypes within each region (parsimony network) and the high level of genetic differentiation between the regions (mean F(ST) = 0.417) indicate that genetic divergence Occurred following the isolation of the two regions. Therefore, the genetic differentiation between regions wits shaped during the Pleistocene, especially during the last glacial and inter and postglacial periods. In addition, Our multilocus analysis showed that populations in central and northern Japan were completely isolated after they split. Geographic separation and subsequent restricted migration events among mountains could explain this isolation history between regions. Furthermore, genetic drift in the reduced populations would remove evidence of occasional migration, emphasizing the isolation history. Therefore, Our application of a demographic model demonstrated the Pleistocene origin of geographic differentiation statistically and provided a plausible migration history for C. nipponica.

    DOI: 10.1093/molbev/msp128

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  • Molecular Evolution of Phytochromes in Cardamine nipponica (Brassicaceae) Suggests the Involvement of PHYE in Local Adaptation 査読

    Hajime Ikeda, Noriyuki Fujii, Hiroaki Setoguchi

    GENETICS   182 ( 2 )   603 - 614   2009年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:GENETICS  

    Given that plants are sessile organisms, traits involved in adapting to local environments and/or in monitoring the surrounding environment, such as having photoreceptors, are significant targets of natural Selection in plant evolution. To assess the intraspecific adaptive evolution of photoreceptors, we investigated sequence variations in four phytochrome genes (PHYA-C and PHYE) of cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. The genealogies of haplotypes and genetic differentiations showed inconsistent patterns of evolution across phytochromes, suggesting that evolutionary forces were distinct in phytochromes of C. nipponica. An overall low level of nucleotide diversity in phytochrome genes suggests that. the evolution of phytochromes is constrained by purifying selection within C. nipponica, which is consistent with previous findings on phytochromes. However, PHYE alone exhibited a non-neutral pattern of polymorphisms (Tajima's D = 1.91, P<0.05) and an accumulations of nonsynonymous substitutions between central and northern Japan. In particular, the PHY domain, which plays ail important role in stabilizing the active form (Pfr) of phytochromes, harbored a specific nonsynonymous fixation between regions. Thus, our finding indicates that local adaptation is involved in the evolution of PHYE in C. nipponica and is the first to Suggest the involvement of PHYE in local adaptation.

    DOI: 10.1534/genetics.109.102152

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  • Consistent geographic structure among multiple nuclear sequences and cpDNA polymorphisms of Cardamine nipponica Franch. et Savat. (Brassicaceae) 査読

    Hajime Ikeda, Kei Senni, Noriyuki Fujii, Hiroaki Setoguchi

    MOLECULAR ECOLOGY   17 ( 13 )   3178 - 3188   2008年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY  

    Molecular phylogeography has inferred the history of differentiation between regions and/or among populations following the Pleistocene climatic oscillations, mostly based on the genetic structure of organelle DNA. However, such genetic structure only reflects the history of a single gene, and studies based on single-copy genes of nuclear DNA (nDNA) are required for phylogeography, although their efficiency remains unclear. To examine the utility of nDNA loci, the genetic structures of three genes from Cardamine nipponica, which is closely related to the model species Arabidopsis thaliana, were elucidated: the nDNA genes DET1, PHYA, PHYE, as well as chloroplast DNA (cpDNA). In 279 individuals collected from throughout the range of the species, strong genetic differentiation between northern and central Japan was found for all loci. This result suggested that populations in central Japan experienced a different history from those in northern Japan during the Pleistocene climatic oscillations. In addition, the evidence of refugia at the edges of the distribution, where the genetic structure was less influenced by colonization following range expansion, was shown for several loci. The specific genetic structure within the southernmost populations of northern Japan suggested that this region was also isolated during range expansion. Hence, the consistent history among loci and a more detailed history from several loci indicated that cpDNA can represent the history of vicariance and demonstrated the efficiency of single-copy nuclear genes in phylogeography.

    DOI: 10.1111/j.1365-294X.2008.03821.x

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  • Post-glacial range fragmentation is responsible for the current distribution of Potentilla matsumurae Th. Wolf (Rosaceae) in the Japanese archipelago 査読

    Hajime Ikeda, Kei Senni, Noriyuki Fujii, Hiroaki Setoguchi

    JOURNAL OF BIOGEOGRAPHY   35 ( 5 )   791 - 800   2008年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Aim We aimed to elucidate how the current geographic distribution of alpine plants in the Japanese archipelago was shaped during Quaternary climatic oscillations, using Potentilla matsumurae as a case study. According to previous phylogeographic studies, post-glacial range fragmentation (vicariance scenario) and stepwise migration (dispersal scenario) are both possible. We thus aimed to assess which scenario is more probable for the distribution changes of alpine plants in the Japanese archipelago.
    Location The alpine zone in the Japanese archipelago.
    Methods Using amplified fragment length polymorphism we determined the genotype of 161 individuals of P. matsumurae from 22 populations. Relationships among individuals and populations were examined using principal coordinates analysis and a neighbour-joining (NJ) tree, respectively. To examine the genetic population structure, we performed analysis of molecular variance (AMOVA) and STRUCTURE analysis.
    Results Differentiation between central Honshu and northern Japan was not very strong based on the principal coordinates analysis among individuals, the NJ tree of populations (59% bootstrap support), or AMOVA (12% of genetic variation). Moreover, structure analysis did not detect clear geographic differentiation across populations. Although the populations in central Honshu were structured geographically (Mantel test: r = 0.45, P < 0.005; NJ tree), those in northern Japan did not exhibit geographic structure regardless of geographic distance (Mantel test: r = 0.26, P = 0.03; NJ tree). Population relationships in the NJ tree did not always reflect the geographic location.
    Main conclusions The current geographic structure of P. matsumurae could not be explained by stepwise migration. This suggests that a single continuous distribution during the last glacial period was later fragmented, perhaps by recovering forest, during the post-glacial period, resulting in the current distribution and phylogeographic structure of P. matsumurae. Our data support the vicariance scenario.

    DOI: 10.1111/j.1365-2699.2007.01828.x

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  • Phylogeography and refugia of the Japanese endemic alpine plant, Phyllodoce nipponica Makino (Ericaceae) 査読

    Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF BIOGEOGRAPHY   34 ( 1 )   169 - 176   2007年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:BLACKWELL PUBLISHING  

    Aim This study aims to elucidate the phylogeography of the Japanese endemic alpine plant, Phyllodoce nipponica Makino (Ericaceae) and to infer the location of refugia of alpine plants in Japan during climatic oscillations.
    Location Alpine zone in the Japanese archipelago.
    Methods We determined the chloroplast (cp) DNA haplotypes of 155 individuals (22 populations) based on sequence data from the trnL-F and trnT-L intergenic spacers and the trnL intron, whose phylogenetic relationships were analysed using the program TCS. To examine the genetic structure, analysis of molecular variance (AMOVA) was carried out and the population differentiation was shown by the parameters G(ST) and N-ST.
    Results The haplotype composition and the results of AMOVA showed that populations in the Japanese Central Mountain Region (JCMR) and in the westernmost region were highly divergent (18.8%). The diversity within populations was very high in the JCMR (h(S) = 0.421); less variation was found within populations located in other regions at lower elevations.
    Main conclusions Phyllodoce nipponica survived climatic changes during the Quaternary in the JCMR and the westernmost region. Most of the distribution range was colonized during only one range expansion. The source location from which the range expansion occurred was unclear.

    DOI: 10.1111/j.1365-2699.2006.01577.x

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  • Refugia of Potentilla matsumurae (Rosaceae) located at high mountains in the Japanese archipelago 査読

    Hajime Ikeda, Kei Senni, Noriyuki Fujii, Hiroaki Setoguchi

    MOLECULAR ECOLOGY   15 ( 12 )   3731 - 3740   2006年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:BLACKWELL PUBLISHING  

    Molecular phylogeographic studies have revealed the genetic patterns and glacial-interglacial history of many plant and animal species. To infer the Quaternary history of alpine plants in the Japanese archipelago, which is poorly known, we investigated 203 individuals of Potentilla matsumurae and its varieties from 22 populations. We found 11 haplotypes based on approximately 1400 bp of two intergenetic spacers in chloroplast DNA (trnT-L and rpl20-rps20). The distribution of these haplotypes was geographically structured, which was supported by haplotype composition, principal component analysis, and unweighted pair group method with arithmetic mean (UPGMA), and N-ST (0.71) was significantly greater than G(ST) (0.68). In addition to the positive correlation between genetic and geographic distance (Mantel test, r = 0.497, P < 0.001), an abrupt genetic change was detected between mountains in central Honshu and the Tohoku region. This genetic boundary was further supported by analysis of molecular variance (AMOVA), and high variation (54.0%) was explained by differences on either side of this boundary. Moreover, haplotypes in central Honshu were thought to have diverged, based on an outgroup comparison. These results suggest that mountains in central Honshu served as refugia during the Quaternary climatic oscillation, although the results could not reveal the history of most mountains in the Tohoku region and Hokkaido. Nevertheless, following floristic studies, our results indicate that alpine plants in Japan experienced a history different from that in Europe; i.e. they retreated into refugia during warm periods to avoid forest development, rather than glaciers.

    DOI: 10.1111/j.1365-294X.2006.03054.x

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  • Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data

    Haruna Sata, Midori Shimizu, Takaya Iwasaki, Hajime Ikeda, Akiko Soejima, Andrey E. Kozhevnikov, Zoya V. Kozhevnikova, Hyoung-Tak Im, Su-Kil Jang, Takayuki Azuma, Atsushi J. Nagano, Noriyuki Fujii

    Journal of Plant Research   2021年9月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    DOI: 10.1007/s10265-021-01339-8

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    その他リンク: https://link.springer.com/article/10.1007/s10265-021-01339-8/fulltext.html

  • Phylogeography of Pulsatilla cernua (Ranunculaceae), a grassland species, in Japan. 国際誌

    Asuka Takaishi, Andrey E Kozhevnikov, Zoya V Kozhevnikova, Hajime Ikeda, Noriyuki Fujii, Akiko Soejima

    Ecology and evolution   9 ( 12 )   7262 - 7272   2019年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    The genetic diversity and structure of Pulsatilla cernua, a continental-grassland relict, were investigated using variations in chloroplast DNA (cpDNA) and microsatellites of nuclear DNA. In the analyses of three cpDNA regions, 17 haplotypes were found in 24 populations of P. cernua from Japan, Korea, and Russia. Although the route and time of migration between the continent of Asia and Japan could not be well resolved, the cpDNA haplotype network suggests the existence of several ancient lineages in Japan and a recent secondary migration from Japan to the continent. Microsatellite analyses did not indicate genetic structure among the Japanese populations, indicating the existence of gene flow across the distribution area until recently. These results indicate that the present fragmentation of P. cernua in Japan may reflect a rapid, recent reduction from a previously large, continuous distribution.

    DOI: 10.1002/ece3.5298

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  • Importance of Beringia for the divergence of two northern Pacific alpine plants, Phyllodoce aleutica and Phyllodoce glanduliflora (Ericaceae) 査読

    Hajime Ikeda, Hiroaki Setoguchi

    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY   122 ( 2 )   249 - 257   2017年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    The Pleistocene glaciations largely influenced species distributions and caused allopatric divergence. Multiple biogeographic processes have contributed to the diversification of the alpine flora around the coastal rim of the north Pacific, which includes survival in Beringian refugia, dispersal between East Asia and North America via the Bering land bridge and range division by continental ice sheets in North America. To assess the history of alpine plants in the northern Pacific Rim, we address the divergence of two alpine shrub species, Phyllodoce aleutica and P. glanduliflora (Ericaceae). Species trees based on sequences of 21 nuclear loci revealed that they are sister species (bootstrap support = 89 and posterior probability = 0.74). Model-based analyses of their speciation history demonstrated that P. aleutica and P. glanduliflora likely diverged without gene flow during the middle/late Middle Pleistocene (c. 307-209 kya). In addition, the inference of ancestral areas on the species tree indicates that their speciation occurred in Alaska, from which P. aleutica spread into East Asia and P. glanduliflora into North America. Accordingly, our study suggests that geographic isolation in separate areas within Beringia played important roles for diversification of alpine plants in the northern Pacific Rim.

    DOI: 10.1093/biolinnean/blx071

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  • Genetic structure of Hepatica nobilis var. japonica, focusing on within population flower color polymorphism 査読

    Shinichiro Kameoka, Hitoshi Sakio, Harue Abe, Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   130 ( 2 )   263 - 271   2017年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER JAPAN KK  

    How phenotypic or genetic diversity is maintained in a natural habitat is a fundamental question in evolutionary biology. Flower color polymorphism in plants is a common polymorphism. Hepatica nobilis var. japonica on the Sea of Japan (SJ) side of the Japanese mainland exhibits within population flower color polymorphism (e.g., white, pink, and purple), while only white flowers are observed on the Pacific Ocean (PO) side. To determine the relationships between flower color polymorphism, within and among populations, and the genetic structure of H. nobilis var. japonica, we estimated the genetic variation using simple sequence repeat (SSR) markers. First, we examined whether cryptic lineages corresponding to distinct flower colors contribute to the flower color polymorphisms in H. nobilis var. japonica. In our field observations, no bias in color frequency was observed among populations on Sado Island, a region with high variation in flower color. Simple sequence repeat (SSR) analyses revealed that 18% of the genetic variance was explained by differences among populations, whereas no genetic variation was explained by flower color hue or intensity (0% for both components). These results indicate that the flower color polymorphism is likely not explained by cryptic lineages that have different flower colors. In contrast, populations in the SJ and PO regions were genetically distinguishable. As with the other plant species in these regions, refugial isolation and subsequent migration history may have caused the genetic structure as well as the spatially heterogeneous patterns of flower color polymorphisms in H. nobilis var. japonica.

    DOI: 10.1007/s10265-016-0893-1

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  • From the north into the Himalayan-Hengduan Mountains: fossil-calibrated phylogenetic and biogeographical inference in the arctic-alpine genus Diapensia (Diapensiaceae) 査読

    Yan Hou, Charlotte Sletten Bjora, Hajime Ikeda, Christian Brochmann, Magnus Popp

    JOURNAL OF BIOGEOGRAPHY   43 ( 8 )   1502 - 1513   2016年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY  

    AimMany arctic species are believed to be descendants from ancestors that migrated northwards from high mountains during the formation of the modern arctic biome 2-3 million years ago (Ma). Here, we test whether this hypothesis is consistent with the biogeographical history of the arctic-alpine genus Diapensia, which shows a disjunction between the Arctic and the Himalayan-Hengduan Mountains (HHM).
    LocationThe Arctic/sub-Arctic and the HHM.
    MethodsWe used the plastid DNA (pDNA) sequences matK and rbcL and seven Ericales fossils to date the origin of Diapensia. Sequences of four pDNA markers and the nuclear ribosomal internal transcribed spacer from 56 Diapenisa accessions were then used to reconstruct the phylogenetic relationships and time of divergence among Diapensia species.
    ResultsDiapensia consists of three major clades; two corresponding to the two arctic species, and one containing the two HHM species sampled. Both the pDNA tree and the species tree resolved the amphi-Beringian D. obovata as sister to a clade that included D. lapponica that has an amphi-Atlantic distribution and the HHM clade. The two arctic species were estimated to have originated in the Middle Miocene-Early Pliocene (D. obovata: 8.3Ma, 95% highest posterior probability density (HPD) 4.0-13.5Ma; D. lapponica: 7.1Ma, 95% HPD 4.1-10.0Ma), long before the formation of the modern arctic biome. In contrast, species divergence in the HHM clade was found to be very recent (0.5Ma, 95% HPD 0.2-0.9Ma; Early-Middle Pleistocene).
    Main conclusionsOur results reject an HHM origin of the arctic Diapensia and rather suggest that the ancestor of the D. lapponica/HHM clade migrated southwards into the HHM. This study adds to a growing body of evidence suggesting that arctic plant lineages have diverse origins in time and space.

    DOI: 10.1111/jbi.12715

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  • Historical biogeography of river-weeds (Podostemaceae) 査読

    Satoshi Koi, Hajime Ikeda, Rolf Rutishauser, Masahiro Kato

    AQUATIC BOTANY   127   62 - 69   2015年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    Podostemaceae are unusual aquatic angiosperms growing as haptophytes in extreme habitats, i.e., rapids and waterfalls. They originated with an ecological shift from terrestrial life, followed by dispersal and diversification. It has been argued that the Tristichoideae originated on the Gondwana and diversified on the drifting continents. We aimed to test this hypothesis, focusing on the place of origin and the frequency and direction of dispersal. We used a Maximum Likelihood (ML) analysis of phylogenetic relationships and comparative morphology for Podostemaceae. The results of the ML analysis showed that the family originated and then diverged to subfamilies Podostemoideae and Weddellinoideae in America, while the Tristichoideae most likely originated in Asia. Comparison with the sister family Hypericaceae indicated that Tristichoideae exhibit plesiomorphic states for all the morphological characters but pollen aperture, whereas Podostemoideae have apomorpic states. Under the island biogeography model, an Asian origin of Podostemaceae may be likely. Those American- and Asian-origin scenarios are contradictory and need further study. The biogeography of the major clades was shaped by several intercontinental dispersals followed by diversification in the colonized continents. A few dispersals happened on the continents of Africa, America and Asia, resulting in the dual biogeography of the continents. Repetition of diversification-dispersal-diversification is suggested by paraphyletic parental groups at higher and lower (species) taxonomic levels. (C) 2015 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.aquabot.2015.08.003

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  • Persistent history of the bird-dispersed arctic-alpine plant Vaccinium vitis-idaea L. (Ericaceae) in Japan 査読

    Hajime Ikeda, Yusuke Yoneta, Hiroyuki Higashi, Pernille Bronken Eidesen, Viachenslav Barkalov, Valentin Yakubov, Christian Brochmann, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   128 ( 3 )   437 - 444   2015年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER JAPAN KK  

    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.

    DOI: 10.1007/s10265-015-0709-8

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  • Molecular phylogeny of Shortia sensu lato (Diapensiaceae) based on multiple nuclear sequences 査読

    Hiroyuki Higashi, Hajime Ikeda, Hiroaki Setoguchi

    PLANT SYSTEMATICS AND EVOLUTION   301 ( 2 )   523 - 529   2015年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER WIEN  

    Molecular phylogenetics is commonly used to perform accurate taxonomic classification. Furthermore, nuclear multilocus sequences have been applied to resolve ambiguous phylogenetic relationships based on conventional markers such as chloroplast and nuclear ribosomal DNA. Here, we reconstructed the phylogenetic tree of Diapensiaceae to revise the traditional classification of the genus Shortia sensu lato (s.l.), which includes Shortia sensu stricto (s.s.) and Schizocodon; whether the latter taxon is treated as an independent genus or includes Shortia s.l. has been disputed since its first description. The phylogeny based on eight nuclear markers developed for this study indicated that Shortia s.l. is not a monophyletic group and that Schizocodon and Shortia s.s. are reciprocally monophyletic. In addition, Schizocodon would be sister to other genus Diapensia despite their morphological differentiation. Thus, our data suggest that Schizocodon represents an independent genus. Our study demonstrated that multiple nuclear loci can resolve obscure phylogenetic relationships determined using conventional markers.

    DOI: 10.1007/s00606-014-1088-7

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  • Polymorphisms of E1 and GIGANTEA in wild populations of Lotus japonicus (vol 127, pg 651, 2014) 査読

    Tomomi Wakabayashi, Hana Oh, Masayoshi Kawaguchi, Kyuya Harada, Shusei Sato, Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   128 ( 1 )   221 - 221   2015年1月

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    記述言語:英語   出版者・発行元:SPRINGER JAPAN KK  

    DOI: 10.1007/s10265-014-0671-x

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  • Polymorphisms of E1 and GIGANTEA in wild populations of Lotus japonicus 査読

    Tomomi Wakabayashi, Hana Oh, Masayoshi Kawaguchi, Kyuya Harada, Shusei Sato, Hajime Ikeda, Setoguchi Hiroaki

    JOURNAL OF PLANT RESEARCH   127 ( 6 )   651 - 660   2014年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER JAPAN KK  

    In plants, timing of flowering is an essential factor that controls the survival rates of descendants. The circadian clock genes E1 and GIGANTEA (GI) play a central role in transmitting signals to FLOWERING LOCUS T (FT) in leguminous plants. Lotus japonicus is a wild Japanese species that ranges from northern Hokkaido to the southern Ryukyus and exhibits a wide range in terms of the time between seeding and first flowering. In this study, we first identified LjGI and analyzed polymorphisms of LjE1 and LjGI among wild populations covering the entire distribution range of this species in Japan. LjGI had a coding sequence (CDS) length of 3495 bp and included 14 exons. The homologies of DNA and amino acid sequences between LjGI and GmGI were 89 and 88 % (positive rate was 92 %), respectively. LjE1 harbored five nucleic acid changes in a 552 bp CDS, all of which were nonsynonymous; four of the changes were located in the core function area. LjE1 alleles exhibited partial north-south differentiation and non-neutrality. In contrast, the LjGI harbored one synonymous and one nonsynonymous change. Thus, our study suggests that LjE1 may be involved in the control of flowering times, whereas LjGI may be under strong purifying selection.

    DOI: 10.1007/s10265-014-0649-8

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  • Phylogeographical study of the alpine plant Cassiope lycopodioides (Ericaceae) suggests a range connection between the Japanese archipelago and Beringia during the Pleistocene 査読

    Hajime Ikeda, Hiroyuki Higashi, Valentin Yakubov, Vyacheslav Barkalov, Hiroaki Setoguchi

    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY   113 ( 2 )   497 - 509   2014年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Given that East Asia is located south-west of Beringia and was less glaciated during the Pleistocene, species at higher latitudes were able to expand their range in this region during climate cooling. Although southward migration is an inevitable colonization process, the biogeographical history of the disjunct ranges of higher-latitude species in East Asia has been investigated less extensively. Here, we assess whether their disjunct distributions in the Japanese archipelago connected sufficiently with Beringia or persisted in isolation following their establishment. Sequences of nine nuclear loci were determined for Cassiope lycopodioides (Ericaceae) from the Japanese archipelago as well as its surrounding areas, Kamchatka and Alaska. According to the geographical pattern of genetic diversity, the northern populations from Kamchatka to the northern part of the Japanese archipelago were similar genetically and were differentiated from populations in central Japan. Our study suggested that the distribution of C.lycopodioides was connected between the northern part of the Japanese archipelago and south-western Beringia due to Pleistocene climate cooling. Conversely, central Japan harboured a disjunct range after its establishment. These inferences suggest that widespread range expansion in northern East Asia was plausible for species distributed in Beringia.(c) 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 497-509.

    DOI: 10.1111/bij.12342

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  • Lineage diversification and hybridization in the Cayratia japonica- Cayratia tenuifolia species complex 査読

    Naoko Ishikawa, Hajime Ikeda, Ting-shuang Yi, Eriko Takabe-Ito, Hiroshi Okada, Hirokazu Tsukaya

    MOLECULAR PHYLOGENETICS AND EVOLUTION   75   227 - 238   2014年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    The Cayratia japonica-Cayratia tenuifolia species complex (Vitaceae) is distributed from temperate to tropical East Asia, Southeast Asia, India, and Australia. The spatiotemporal diversification history of this complex was assessed through phylogenetic and biogeographic analyses. Maximum parsimony, neighbor-joining, and maximum likelihood methods were used to analyze sequences of one nuclear (AS1) and two plastid regions (trnL-F and trnC-petN). Bayesian dating analysis was conducted to estimate the divergence times of clades. The likelihood method LAGRANGE was used to infer ancestral areas. The Asian C. japonica and C tenuifolia should be treated as an unresolved complex, and Australian C japonica is distinct from the Asian C japonica-C tenuifolia species complex and should be treated as separate taxa. The Asian C. japonica-C tenuifolia species complex was estimated to have diverged from its closest relatives during the Late Eocene (35.1 million years ago [Ma], 95% highest posterior densities [HPD] = 23.347.3 Ma) and most likely first diverged in mid-continental Asia. This complex was first divided into a northern clade and a southern clade during the middle Oligocene (27.3 Ma; 95% HPD = 17.4-38.1 Ma), which is consistent with a large southeastward extrusion of the Indochina region relative to South China along the Red River. Each of the northern and southern clades then further diverged into multiple subclades through a series of dispersal and divergence events following significant geological and climatic changes in East and Southeast Asia during the Miocene. Multiple inter-lineage hybridizations among four lineages were inferred to have occurred following this diversification process, which caused some Asian lineages to be morphologically cryptic. (C) 2014 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.ympev.2014.01.027

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  • Erratum to: Polymorphisms of E1 and GIGANTEA in wild populations of Lotus japonicus (Journal of Plant Research, 10.1007/s10265-014-0649-8)

    Tomomi Wakabayashi, Hana Oh, Masayoshi Kawaguchi, Kyuya Harada, Shusei Sato, Hajime Ikeda, Hiroaki Setoguchi

    Journal of Plant Research   128   221   2014年1月

  • A multilocus sequencing approach reveals the cryptic phylogeographical history of Phyllodoce nipponicaMakino (Ericaceae) 査読

    Hajime Ikeda, Hiroaki Setoguchi

    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY   110 ( 1 )   214 - 226   2013年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to re-examine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a discordant pattern compared to those of other alpine plants. The geographical structure of sequence variation at five nuclear loci was not consistent with that of cpDNA and showed differentiation between the northern and southern parts of the range of this species. Its demographic history inferred from the isolation-with-migration model suggests that the north-south divergence originated from Pleistocene vicariance. In addition, the demographic parameters showed a lack of chloroplast-specific gene flow, suggesting that stochastic variance in genealogy resulted in the discordant geographical structure. Thus, P.nipponica probably experienced Pleistocene vicariance between its southern and northern range parts in concordance with other alpine plants in the Japanese archipelago. The findings of the present study demonstrates the importance of using a multilocus approach for inferring population dynamics, as well as for reconciling discordant phylogeographical patterns among species.(c) 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 214-226.

    DOI: 10.1111/bij.12116

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  • Multiple introgression events and range shifts in Schizocodon (Diapensiaceae) during the Pleistocene 査読

    Hiroyuki Higashi, Shota Sakaguchi, Hajime Ikeda, Yuji Isagi, Hiroaki Setoguchi

    BOTANICAL JOURNAL OF THE LINNEAN SOCIETY   173 ( 1 )   46 - 63   2013年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Range shifts during the Pleistocene shaped the unique phylogeographical structures of numerous species. Accompanying species migration, sister taxa may have experienced multiple introgression events. Here, we report the signature of introgression events in multiple areas in Schizocodon, herbs endemic to Japan, using amplified fragment length polymorphism (AFLP) fingerprinting and plastid DNA haplotyping in 48 populations. Although the present distributions of S.soldanelloides and S.ilicifolius are mainly allopatric, the species share plastid DNA haplotypes in each region (north-eastern, north-central, south-central and south-western Japan); in contrast, the specific groups were highly supported by AFLP analyses. These results support the occurrence of multiple introgression events in Schizocodon. Notably, the disjunct plastid haplotypes found only in S.ilicifolius var. intercedens suggest complete plastid DNA replacement at local areas from S.soldanelloides into S.ilicifolius var. ilicifolius. Furthermore, we found that S.soldanelloides experienced range contraction and expansion during glacial and interglacial cycles based on mismatch distribution analysis and ecological niche modelling. Based on several pieces of evidence, our study supports the idea that historical range shifts associated with Pleistocene climatic oscillations favoured multiple and regional introgression events in Schizocodon.(c) 2013 The Linnean Society of London.

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  • Recent colonization by a coastal plant of inland habitats at an ancient freshwater lake, Lake Biwa: multilocus sequencing and a demographic history of Lathyrus japonicus (Fabaceae) 査読

    Tatsuo Ohtsuki, Hajime Ikeda, Hiroaki Setoguchi

    ECOLOGY AND EVOLUTION   3 ( 8 )   2600 - 2611   2013年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Ancient lakes have been recognized as "long-term isolated islands" in terrestrial ecosystems. Lake Biwa, one of the few ancient lakes that formed around 4 million years ago, harbors many coastal species that commonly inhabit seashores. The beach pea, Lathyrus japonicus, is a typical coastal species of this freshwater lake, where morphological, physiological, and genetic differentiations have been reported between Biwa and coastal populations. Whether Biwa populations were isolated for long periods throughout Pleistocene climatic oscillations and subsequent range shifts is unclear. We assessed population genetic structure and demography of beach pea in this ancient freshwater lake using the sequences of eight nuclear loci. The results of STRUCTURE analyses showed evidence of admixture between Biwa and coastal populations, reflecting recent gene flow. The estimated demographic parameters implemented by the isolation with migration model (IM model) revealed a recent divergence (postglacial period) of Biwa populations, with some gene flow from Biwa to coastal populations. In addition, Biwa populations were significantly smaller in size than the ancestral or coastal populations. Our study suggests that a Holocene thermal maximum, when transgression could allow seeds from coastal plants to access Lake Biwa, was involved in the origin of the Biwa populations and their genetic divergence. Thus, coastal populations might have migrated to Lake Biwa relatively recently. Our study concluded that ancestral migrants in Lake Biwa were derived from small founding populations and accelerated genetic isolation of Biwa populations during short-term isolation.

    DOI: 10.1002/ece3.654

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  • Phylogeographic Study of Phyllodoce aleutica (Ericaceae) in the Japanese Archipelago 査読

    IKEDA Hajime, IKEDA Hajime, SETOGUCHI Hiroaki

    Bull Natl Mus Nat Sci Ser B Bot   39 ( 2 )   87 - 94   2013年5月

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    記述言語:英語  

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  • Population fragmentation causes randomly fixed genotypes in populations of Arabidopsis kamchatica in the Japanese Archipelago 査読

    Hiroyuki Higashi, Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   125 ( 2 )   223 - 233   2012年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER JAPAN KK  

    Populations of arctic alpine plants likely disappeared and re-colonised several times at the southern edge of their distributions during glacial and interglacial cycles throughout the Quaternary. Range shift and population fragmentation after a glacial period would affect the genetic structure of such plants in southernmost populations. We aimed to elucidate how climatic oscillations influenced the population subsistence of alpine plants in the Japanese Archipelago as one of the southernmost populations, by inferring the genetic structure of Arabidopsis kamchatica subsp. kamchatica and the intraspecific littoral taxon, subsp. kawasakiana. We identified genotypes based on the haplotypes of five nuclear genes and two chloroplast DNA spacers for 164 individuals from 24 populations. Most populations harboured only one private genotype, whereas few polymorphisms were found in each population. Two genetic genealogies were found, suggesting that northern Japanese populations of alpine subsp. kamchatica, subsp. kawasakiana and the northerly subsp. kamchatica in eastern Russia and Alaska clustered and differentiated from populations in central Honshu, western Japan and Taiwan. During climatic oscillations, the genetic structure of extant southernmost populations would have been shaped by strong genetic drift under population fragmentation and randomly fixed to a single genotype among their ancestral polymorphisms.

    DOI: 10.1007/s10265-011-0436-8

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  • Erratum to: Population fragmentation causes randomly fixed genotypes in populations of Arabidopsis kamchatica in the Japanese Archipelago (J Plant Res, 10.1007/s10265-011-0436-8) 査読

    Hiroyuki Higashi, Hajime Ikeda, Hiroaki Setoguchi

    Journal of Plant Research   125 ( 2 )   235 - 236   2012年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1007/s10265-011-0443-9

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  • Genetic structure of the critically endangered plant Tricyrtis ishiiana (Convallariaceae) in relict populations of Japan 査読

    Hiroaki Setoguchi, Yuki Mitsui, Hajime Ikeda, Naofumi Nomura, Atsushi Tamura

    CONSERVATION GENETICS   12 ( 2 )   491 - 501   2011年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Tricyrtis ishiiana is a relic endemic plant taxon of the Convallariaceae that inhabits two nearby gorges in Kanagawa Prefecture, Japan. The distribution range and number of populations are thought to have been reduced to the present refugial populations during the Quaternary climatic oscillations. Because of its showy flowers, this plant has faced illegal removal from its natural habitats for horticultural use and has been designated a critically endangered species (class IA). In this study, we analyzed the genetic structure of the relict populations of T. ishiiana in order to contribute to the conservation strategies of the prefectural government. Our analyses of nine nuclear microsatellite loci detected high genetic diversity (H (E) = 0.704 and H (O) = 0.541) for the two populations. The two populations were slightly differentiated (R (ST) = 0.032), accompanied by faint substructure across the populations (K = 3). In addition, each population exhibited spatial genetic structuring. The relatively low inbreeding coefficient for both populations together (F (IS) = 0.233) and each population separately (F (IS) = 0.217-0.246) may be attributable to crossing among descendants within a population along with occasional gene flow between the populations. These results suggested that the extant populations have not experienced a severe bottleneck. The two extant populations were genetically differentiated at a very low level, accompanied by occasional pollen flow via pollinators and/or seed dispersal by gravity in the mountainous environment. Occasional gene exchange between the populations has allowed T. ishiiana to harbor high genetic diversity despite being a relic plant confined to two small refugial populations.

    DOI: 10.1007/s10592-010-0156-y

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  • Long-term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa, Japan 査読

    Asuka Noda, Yuki Mitsui, Hajime Ikeda, Hiroaki Setoguchi

    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY   102 ( 1 )   51 - 66   2011年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL  

    Lake Biwa is an ancient freshwater lake that was formed approximately 4 Mya and harbours many coastal plants that commonly inhabit the seashore. We used chloroplast DNA haplotype analysis using two spacer sequences and simple sequence repeat (SSR) analysis using eight nuclear microsatellite markers to detect genomic signatures indicating long-term isolation of inland populations of Calystegia soldanella in Lake Biwa from coastal populations. We used 348 samples from 63 populations for haplotype analysis and 478 samples from 27 populations for SSR analysis covering the inland and coastal distribution of the species. We detected seven haplotypes, and the distribution pattern of these haplotypes was geographically highly structured between Lake Biwa and the coast. Nuclear SSR analysis also supported genetic differentiation between Lake Biwa and coastal populations (analyses of molecular variance, 43%), and the grouping of Lake Biwa and coastal populations by a Neighbour-joining tree. In addition, genetic diversity of the inland populations (mean H-E = 0.153) was significantly lower than that of coastal populations (mean H-E = 0.328). These results suggested that inland populations at Lake Biwa have been isolated from coastal populations for a very long time. The inland populations most likely experienced a bottleneck effect, resulting in sufficient in situ genetic divergence to clearly distinguish them from coastal populations. (c) 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 51-66.

    DOI: 10.1111/j.1095-8312.2010.01554.x

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  • Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in Cardamine nipponica (Brassicaceae) 査読

    Hajime Ikeda, Noriyuki Fujii, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   124 ( 1 )   85 - 92   2011年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER TOKYO  

    Various photoreceptors in plants are used to monitor important environmental light signals and regulate plant development. Despite their functional importance, recent studies have demonstrated that red/far-red absorbing phytochromes or blue/UV-A absorbing cryptochromes are involved in local adaptation within a species' range. In the present study, to exemplify the intraspecific photoreceptor evolutionary pattern, the genetic structures of cryptochrome genes (CRY1 and CRY2) in Cardamine nipponica (Brassicaceae), of which PHYE, a gene coding one of the phytochromes, was found to be involved in local adaptation between central and northern Japanese populations. Although clear genetic differentiations between central and northern Japan were detected (CRY1: F (ST) = 0.63, CRY2: F (ST) = 0.53), overall nucleotide diversity was very low (CRY1: pi (Total) = 0.0014, CRY2: pi (Total) = 0.0013), and the polymorphism patterns were neutral (CRY1: Tajima's D = 0.084, P = 0.32, CRY2: D = -0.014, P = 0.39). Therefore, the involvement of cryptochromes in the adaptation to local environments is difficult to postulate. Consequently, this study along with our previous findings suggest that intraspecific photoreceptor gene polymorphisms in C. nipponica were mostly suppressed by purifying selection due to their functional importance as photoreceptors, while some of the photoreceptors may play substantial roles in adaptation to local environments.

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  • Genomic Structure of Lowland and Highland Ecotypes of Arabidopsis halleri subsp. gemmifera (Brassicaceae) on Mt. Ibuki 査読

    IKEDA Hajime, SETOGUCHI Hiroaki, MORINAGA Shin‐ichi

    Act Phytotaxono Geobot   61 ( 1 )   21 - 26   2010年6月

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  • Genetic structure among and within populations of the serpentine endemic Heteropappus hispidus ssp leptocladus (Compositae) 査読

    Takayuki Yokoo, Shiro Kobayashi, Kazuo Oginuma, Kazumi Fujikawa, Yuki Mitsui, Hajime Ikeda, Hiroaki Setoguchi

    BIOCHEMICAL SYSTEMATICS AND ECOLOGY   37 ( 4 )   275 - 284   2009年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:PERGAMON-ELSEVIER SCIENCE LTD  

    Heteropappus hispidus ssp. leptocladus is an edaphic endemic taxon that is confined to serpentine and limestone-derived soils and is allopatrically distributed in three regions of western Japan. In this study, we attempted to detect genomic signatures of seven H. hispidus ssp. leptocladus populations along with eight other subspecies populations using eight nuclear microsatellite loci. The Mantel test supported an isolation by distance model across all H. hispidus populations, thus implying the possibility of parallel evolution for each subspecies. Results from AMOVA recognized relatively larger differentiations in geographic distribution compared to intraspecific taxonomy. Relationships indicated by neighbor-joining phylogenetic tree analysis and population structure generally did not reflect an intraspecific taxonomy. Populations from limestone-derived soil harbored a homogeneous genetic structure with neighboring populations from serpentine-derived soils. These results suggest that the edaphic ecotype may have derived allopatrically while a lack of edaphic constraint existed between serpentine and limestone soils. (C) 2009 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.bse.2009.04.012

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  • Genetic structure of refugial populations of the temperate plant Shortia rotundifolia (Diapensiaceae) on a subtropical island 査読

    Tomomi Dan, Hajime Ikeda, Yuki Mitsui, Yuji Isagi, Hiroaki Setoguchi

    CONSERVATION GENETICS   10 ( 4 )   859 - 867   2009年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Continental island systems harbour relict biota and populations that might have migrated during glacial periods due to the formation of landbridges. Here we analysed the genetic structure of relict populations of the temperate plant Shortia rotundifolia on the subtropical island of Iriomotejima, Japan. This plant, which inhabits riparian environments, is designated "near threatened". Only five extant populations have been found on the island. Our analyses of 10 nuclear microsatellite loci detected genetic diversity of H (E) = 0.488 and H (O) = 0.358 for all populations of S. rotundifolia on the island. A high inbreeding coefficient for all populations together (F (IS) = 0.316) and each population separately (F (IS) = 0.258-0.497) might be attributable to crossing among closely related descendants within a population, an idea that is supported by the relatedness coefficient. These results and an examination of the populations' demographic histories suggest that the extant populations on Iriomotejima have not experienced a recent population bottleneck. The five extant populations were genetically differentiated (F (ST) = 0.283; P < 0.001), suggesting low seed dispersal by gravity and/or low pollen flow via pollinators in the riparian environment. In addition, population differentiation was not related to genetic distance, implying that at one time, ancestral populations might have been distributed over a wider area of the island. However, population fragmentation and range contraction might have occurred at random during the postglacial period.

    DOI: 10.1007/s10592-008-9646-6

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  • High mountains of the Japanese archipelago as refugia for arctic-alpine plants: phylogeography of Loiseleuria procumbens (L.) Desvaux (Ericaceae) 査読

    Hajime Ikeda, Kei Senni, Noriyuki Fujii, Hiroaki Setoguchi

    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY   97 ( 2 )   403 - 412   2009年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:WILEY-BLACKWELL PUBLISHING, INC  

    According to previous phylogeographic studies, high mountains at low latitudes are important areas for the study of the evolutionary history of arctic-alpine plants in surviving the Pleistocene climatic oscillations. To evaluate this hypothesis, we elucidated the genetic structure of the arctic-alpine plant, Loiseleuria procumbens, in the Japanese archipelago, which corresponds to one of the southernmost limits of its distribution, using 152 individuals from 17 populations that covered the entire distribution of the Japanese archipelago and Sakhalin, in addition to samples from Sweden. Based on 854 bp of chloroplast DNA, we detected eight haplotypes. Along with haplotype distribution, strong genetic differentiation between populations in central and northern Japan was elucidated by a neighbour-joining tree (100%) and spatial analysis of molecular variance (79%), which is consistent with other alpine plants in Japan, regardless of the species&apos; range. In addition, the southernmost populations from northern Japan showed specific genetic structure, although the remaining areas of northern Japan and Sakhalin harboured an homogenous genetic structure. Our results suggest that the populations in central Japan persisted for a long time during the Pleistocene climatic oscillation and that genetic divergence occurred in situ, supporting our hypothesis in conjunction with a previous study of another arctic-alpine plant, Diapensia lapponica subsp. obovata. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 403-412.

    DOI: 10.1111/j.1095-8312.2009.01177.x

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  • Isolation and characterization of microsatellite loci in Shortia rotundifolia (Diapensiaceae), an endangered relict plant on the Ryukyu Islands and Taiwan 査読

    Tomomi Dan, Yuki Mitsui, Hajime Ikeda, Yuji Isagi, Hiroaki Setoguchi

    CONSERVATION GENETICS   10 ( 3 )   507 - 509   2009年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Ten microsatellite loci were isolated and characterized for Shortia rotundifolia, a relict temperate plant on the subtropical Ryukyu Islands and Taiwan. The number of alleles ranged from 2 to 21. The expected (H (E)) and observed (H (O)) heterozygosities were 0.027-0.877 and 0.027-0.622, respectively, from 74 individuals on Iriomotejima Island of Ryukyus. One locus exhibited significantly fewer heterozygotes than expected under Hardy-Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in this species may provide a useful tool for population genetics to establish conservation strategy.

    DOI: 10.1007/s10592-008-9551-z

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  • Development and characterization of microsatellite loci in the endangered Tricyrtis ishiiana (Convallariaceae), a local endemic plant in Japan 査読

    Hiroaki Setoguchi, Yuki Mitsui, Hajime Ikeda, Naofumi Nomura, Atsushi Tamura

    CONSERVATION GENETICS   10 ( 3 )   705 - 707   2009年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Nine microsatellite loci were isolated and characterized for the endangered and tertiary relict perennial herb, Tricyrtis ishiiana. The number of alleles ranged from 2 to 33. The expected (H (E)) and observed (H (O)) heterozygosities were 0.207-0.944 and 0.215-0.813, respectively, from 96 individuals on one population. Five loci exhibited significantly fewer heterozygotes than expected under Hardy-Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in this species may provide a useful tool for population genetics to establish conservation strategy.

    DOI: 10.1007/s10592-008-9620-3

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  • The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of Arcterica nana (Maxim.) Makino (Ericaceae) 査読

    Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   122 ( 2 )   141 - 151   2009年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER TOKYO  

    Previous phylogeographic studies of alpine plants in Japan have inferred that populations in central Honshu persisted during the Pleistocene climatic oscillations and suggested interglacial survival in high mountains. However, Arcterica nana (Maxim.) Makino (Ericaceae) exhibits a homogenous genetic structure throughout Japan and may therefore have a unique phylogeographic history. This inconsistency could have resulted from insufficient resolution of previously analyzed chloroplast DNA sequences. Therefore, we conducted a phylogeographic investigation based on amplified fragment length polymorphisms. Using 176 individuals from 21 populations, the relationships among individuals and populations were determined by principal coordinate analysis and a neighbor-joining tree, respectively. In addition, genetic differentiation was estimated using analysis of molecular variance and spatial autocorrelation analysis. These analyses demonstrate a homogenous structure throughout the entire Japanese range, supporting the previous cpDNA phylogeography. Although this genetic structure is inconsistent with those of other alpine plants, it is difficult to postulate that pre-existing genetic differentiation was swamped exclusively within A. nana. Therefore, this homogenous genetic structure may have been caused by the distinct history of populations of A. nana. Specifically, the southern-ward migration and the subsequent continuous populations enabled gene flow throughout the Japanese archipelago during the last glacial period. Thus, our data suggest that alpine plants in the Japanese archipelago did not always experience a shared distribution change following climatic oscillations.

    DOI: 10.1007/s10265-008-0213-5

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  • Survival and genetic divergence of an arctic-alpine plant, Diapensia lapponica subsp. obovata (Fr. Schm.) Hultén (Diapensiaceae), in the high mountains of central Japan during climatic oscillations

    Ikeda, H, K. Senni, N. Fujii, H. Setoguchi

    Plant Systematics and Evolution   272 ( 1-4 )   197 - 210   2008年5月

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    掲載種別:研究論文(学術雑誌)  

    Previous phylogeographic studies of arctic-alpine plants have partly elucidated that alpine areas at the southernmost edges of their distribution have been one of the most important areas for the survival of populations through Quaternary climatic oscillations. To reveal the genetic structure of arctic-alpine plants near the southern edge of their range in East Asia, 159 samples of Diapensia lapponica subsp. obovata (Diapensiaceae) were collected from 22 populations in Japan. Based on 1,134 bp of chloroplast DNA (cpDNA), we determined 10 haplotypes. Neighbor-joining (NJ) analysis, including D. lapponica from Sweden and Schizocodon soldanelloides, revealed that all haplotypes in Japan were monophyletic. Genetic differentiation between populations of central Honshu and northern Japan was strongly supported by the NJ tree (100%), analysis of molecular variance (AMOVA, 68%), and Monmonier&#039;s algorithm (&gt;95%). The most ancestral haplotype rarely occurred in Japan, which implied that the extant genetic structure was not caused by genetic divergence during colonization. Thus, these results suggest that the arctic-alpine plant D. lapponica subsp. obovata survived climatic oscillations in central Honshu. This finding supports the hypothesis that high mountains in temperate regions were important for survival of arctic-alpine plants during Quaternary climatic oscillations. © 2008 Springer-Verlag.

    DOI: 10.1007/s00606-007-0637-8

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  • Phylogeography of Arcterica nana (Ericaceae) suggests another range expansion history of Japanese alpine plants 査読

    Hajime Ikeda, Hiroaki Setoguchi

    JOURNAL OF PLANT RESEARCH   119 ( 5 )   489 - 495   2006年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER TOKYO  

    We conducted a phylogeographic study on the alpine plant Arcterica nana based on haplotypes of chloroplast,DNA. Using a sequence of approximately 1,071 by of intergenic spacers of chloroplast DNA (trnT-L, psbB psbF), we detected 13 haplotypes among 193 individuals sampled from 22 populations. Two dominant haplotypes were distributed over the entire range of this species in Japan, and we found several local private haplotypes. An analysis of molecular variance (AMOVA) indicated no geographic structure within the haplotype distribution. In addition, the genetic distance was not related to its corresponding geographic distance (Mantel test: r= -0.049, P=0.66), indicating a homogeneous geographic structure throughout the entire distribution range in the Japanese archipelago. The most parsimonious explanation for this geographic structure is that A. nana spread across its extant distribution range in the Japanese archipelago through a recent range expansion event. However, this pattern is inconsistent with the previous phylogeography of Japanese alpine plants, which reveals that haplotypes in central Honshu are differentiated from those in more northern regions. Arcterica nana may have experienced a different history from other alpine plants, suggesting that the history of Japanese alpine flora may include at least two different geographic radiation patterns.

    DOI: 10.1007/s10265-006-0012-9

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▼全件表示

MISC

  • 日本のマメ科高山植物―根粒菌共生系の系統と宿主特異性

    川井友裕, 瀬尾直登, 池田啓, 佐藤修正, 矢崎一史, 髙梨功次郎

    日本植物分類学会第16回大会   2017年3月

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    記述言語:日本語   掲載種別:研究発表ペーパー・要旨(全国大会,その他学術会議)  

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  • ミヤマタネツケバナCardamine nipponicaの系統解析とPHYEの分子進化.

    池田啓, Lovisa Gustafson, Christian Brochmann, 瀬戸口浩彰

    日本植物学会第79大会,新潟市, 9月5日〜8日. 2015年   P-025   2015年9月

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    記述言語:日本語   掲載種別:研究発表ペーパー・要旨(全国大会,その他学術会議)  

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  • 周北極‐高山植物エゾツガザクラPhyllodoce caeruleaの系統地理

    池田啓, 阪口翔太, YAKUBOV Valentin, BARKALOV Vyacheslav, 瀬戸口浩彰

    日本植物学会大会研究発表記録   78th   169   2014年9月

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    記述言語:日本語  

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  • 日本産高山植物の比較系統地理

    池田啓, 仙仁径, 藤井紀之, 清水健太郎, 瀬戸口浩彰

    日本生態学会大会講演要旨集   54th   377   2007年3月

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    記述言語:日本語  

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受賞

  • 奨励賞

    2020年5月   日本植物学会  

    池田啓

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  • 奨励賞

    2014年3月   日本植物分類学会  

    池田 啓

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  • 若手奨励賞

    2009年9月   日本植物学会  

    池田 啓

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共同研究・競争的資金等の研究

  • 植物の光受容体フィトクロムの生理的性質の変化が引き起こす種分化機構の検証

    研究課題/領域番号:20K06798  2020年04月 - 2023年03月

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    池田 啓

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    配分額:4420000円 ( 直接経費:3400000円 、 間接経費:1020000円 )

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  • 東北アジアにおける草原性植物群の変遷史からみた日本列島フロラの成立過程の解明

    研究課題/領域番号:17H03721  2017年04月 - 2022年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    藤井 紀行, 副島 顕子, 岩崎 貴也, 池田 啓

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    配分額:17030000円 ( 直接経費:13100000円 、 間接経費:3930000円 )

    今年度は本課題研究の二年目ということで、海外調査は韓国と中国の2カ国で行った。また国内における調査は、九州、中国や東北地方において行った。対象植物しては、これまで満鮮要素とされてきた植物の中からヒロハヤマヨモギ、ツチグリ、タムラソウ、ノカラマツ、オキナグサ、シロスミレ、キスミレなどを中心的に採集および解析を進めた。またその他にもツクシクガイソウ、オケラ、サイヨウシャジン、ヤツシロソウ、キキョウ、シオン、ミヤコアザミ、オカオグルマ、トモエソウ、ヒメユリ、シオガマギク、シラヤマギク、スズサイコなどの採集も行った。解析結果としては、葉緑体DNAのハプロタイプ解析をベースに、シロスミレ、キスミレに関してはRAD-seq, MIG-seq解析を行って解析を進めた。主要な結果として、タムラソウおよびシロスミレの結果を示す。まずタムラソウに関しては、今年度新たに解析を進めた種である。葉緑体DNAハプロタイプ解析を行った結果、9つのタイプが検出され、そのうちタイプAがコモンタイプであり、中国やロシア、韓国、日本国内においても広く分布していた。一方、日本国内の中国地方から長野県にかけての地域では、タイプBが優占しており、興味深い地理的な構造が明らかとなった。さらにハプロタイプ間のネットワーク解析を行った結果、タイプAを中心とした「一斉放散型」のネットワーク図が得られた。この結果は本種が最終氷期といった近年の急速な分布拡大をした歴史的シナリオを支持している。一方、シロスミレの解析においても9つのハプロタイプが検出され、ネットワーク解析を行った結果、2つのグループ(AーEタイプとFーIタイプ)が認識された。両グループの分布はかなりランダムであり重なっていた。このような結果が得られた要因に関して、今後MIG-seq解析を用いて再検討する予定である。

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  • 環太平洋地域における周北極高山植物の起源とベーリンジア・レフュジア仮説の検証

    研究課題/領域番号:26304013  2014年04月 - 2017年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    瀬戸口 浩彰, 池田 啓

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    配分額:13780000円 ( 直接経費:10600000円 、 間接経費:3180000円 )

    アラスカ南部のキーナイ半島を中心とする地域、デナリ国立公園の南部の内陸部における海外調査を実施した。4地点における植物採取を行い、ミネズオウやエゾツツジなど日本列島にも共通して分布する高山植物(計35種)から、DNA解析に使用する試料を収集した(計419サンプル)。海外調査に加え、これまでの調査及び本年の調査で収集した試料からDNAを抽出し、核遺伝子における遺伝的多様性を解析した。本年度はアオノツガザクラに力を入れて解析を進め、日本列島の中部地方・北海道中部及び北海道東部からアラスカまでの3つの遺伝的グループに分かれることが明らかとなった。この成果は2017年3月の植物分類学会で口頭発表した。

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  • 花成遺伝子の多型による開花期の地域適応と種分化機構の解明

    研究課題/領域番号:24247013  2012年04月 - 2016年03月

    日本学術振興会  科学研究費助成事業 基盤研究(A)  基盤研究(A)

    瀬戸口 浩彰, 川口 正代司, 池田 啓

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    配分額:44850000円 ( 直接経費:34500000円 、 間接経費:10350000円 )

    植物が成長相転換を行うタイミングを適切に測ることは、その種の生存に極めて重要なイベントである。発芽から枝葉を茂らせて光合成と成長に専念する栄養成長を、どのタイミングで繁殖成長に切り替えるかは、様々な外的・内的な要因がある。この研究では、日長と温度(春化)という、二つの環境要因に焦点を当てて、ミヤコグサとハマダイコンを用いて研究を行った。ミヤコグサでは基本的に次世代シーケンサーを用いた全ゲノム比較を行って、開花の早晩に関与する遺伝子を探索し、EMF2などの重要な候補遺伝子などの関与を見いだした。ハマダイコンでは、低緯度の系統で抽だいと開花に春化処理が不要であることを見いだした。

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  • モデル生物を利用した野生集団に保持される遺伝的変異の機能解析

    研究課題/領域番号:23657015  2011年 - 2012年

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    池田 啓

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    配分額:3770000円 ( 直接経費:2900000円 、 間接経費:870000円 )

    野生集団が持つ遺伝的変異の機能を解析するために、ミヤマタネツケバナ(Cardamine nipponica)の野生集団に複数のアミノ酸置換を伴った対立遺伝子を持つPHYEに着目した。まず、大腸菌でタンパク質を発現させるためのベクターにPHYEを挿入することに成功した。特に、特定のアミノ酸置換の影響を評価するために、対立遺伝子の間で異なるアミノ酸残基を入れ替えたキメラ配列のコンストラクトを構築することができた。また、植物(シロイヌナズナ)に遺伝子導入し、強発現するためのベクターにPHYEを挿入することに成功した。当初の目的であるタンパク質や植物体における機能解析を終えることができなかったが、これらの成果は今後の研究で野生集団が持つ変異の機能を明らかにするために有効な進展である。

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  • 周極要素植物の緯度傾度に伴う環境適応と進化多様性形成

    研究課題/領域番号:22405013  2010年04月 - 2014年03月

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    瀬戸口 浩彰, 池田 啓, 藤井 紀行, 東 浩司

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    配分額:18070000円 ( 直接経費:13900000円 、 間接経費:4170000円 )

    本研究では、光受容色素タンパク質(フィトクロムなど)の花成に関与する遺伝子が、高緯度~低緯度の環境傾度の中で、機能分化をどのように起こしているか解析した。アブラナ科のCardamine nipponicaとC. bellidifoliaを主体にして用いて、計画通りに知見を得た:高緯度の個体は種を超えてPHYEを特化させており、C. nipponicaの低緯度個体は独自のPHYEアリルを保有していた。また、ツツジ科のツガザクラ属においては、周極要素植物の起源が北にあるという従来仮説を否定する知見を得た。以上の研究はロシア科学アカデミーやノルウエーのオスロ大学との共同研究体制にて遂行した。

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  • 光環境を受容するフィトクロム遺伝子群のゲノム進化がもたらす多様性形成機構の解析

    研究課題/領域番号:21370036  2009年 - 2011年

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    瀬戸口 浩彰, 長谷 あきら, 藤井 紀行, 池田 啓

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    配分額:18720000円 ( 直接経費:14400000円 、 間接経費:4320000円 )

    (1)アブラナ科ミヤマタネツケバナにおけるPHYE遺伝子の南北間分化を比較した。PHYE遺伝子を単離して、クローニングを進め、高機能高変異性を示すN末端側をクローニングすることができた。この構築されたプラスミドは、大腸菌に形質転換することでタンパク質を合成する機能を持つ。
    (2)緯度に応じて開花応答性が大きく異なるマメ科ミヤコグサで、光受容遺伝子群の分化を検証した。PHYA, PHYB, PHYEにおいて多数の非同義的置換が産地間にあり、そのアミノ酸置換の多くはGAFドメインなどの機能中枢に偏在していた。

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  • 高山植物を例にした分断分布に伴うゲノム分化が引き起こす種分化機構の解明

    研究課題/領域番号:07J01858  2007年 - 2009年

    日本学術振興会  科学研究費助成事業 特別研究員奨励費  特別研究員奨励費

    池田 啓

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    配分額:2800000円 ( 直接経費:2800000円 )

    昨年度の結果から、フィトクロムの一つであるPHYEが中部地方と北日本のミヤマタネツケバナにおいて地域適応に関わっていることが示されていた。このPHYEが高山植物において地域適応に重要であることを補完し、PHYEが高山植物一般に地域適応に関わっていることを示すために、以下の2つの研究を進めた。
    1つ目には、フィトクロムとは異なる波長の光を受容するクリプトクロム(CRY)遺伝子が、ミヤマタネツケバナにおける地域適応に関わっているかを検討した。その結果、クリプトクロムは分子進化的には地域適応には関与せず、PHYEのみが重要な受容体であることが強調された。
    2つ目の研究として、他の高山植物においてもミヤマタネツケバナ同様に、PHYEが日本列島における地域適応に関わっていることを検討した。コメバツガザクラ(ツツジ科)からPHYEの遺伝子を単離し、その地理構造を評価した。その結果、コメバツガザクラにおいて、PHYEが緯度に沿った適応に関与している可能性が示された。このことは、コメバツガザクラにおいても、PHYEが南北間での地域適応に関わっていることを示唆された。このようにして、本年度の研究から、日本列島の高山植物における地域適応には、PHYEが重要な役割を果たしていることを強調することができた。PHYE遺伝子の機能は現段階では明確には分かっておらず、その地域適応への関与は本研究により初めて示された。PHYE遺伝子は被子植物に比較的広くみられる。そのため、この発見はPHYE遺伝子が地域適応に関わることで、植物の適応進化に普遍的に重要な因子である可能性を示唆している。

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