Researcher Database

Koh Nakamura
Field Science Center for Northern Biosphere Agro-Ecosystem Research Station Botanic Garden
Associate Professor

Researcher Profile and Settings


  • Field Science Center for Northern Biosphere Agro-Ecosystem Research Station Botanic Garden

Job Title

  • Associate Professor


Research funding number

  • 70532927

J-Global ID

Research Interests

  • Plant phylogeography   Hokkaido   Japanese archipelago   Asian islands   Philippines   Taiwan   Ryukyu Archipelago   Plant phylogenetic systematics   Phytogeography   

Research Areas

  • Life sciences / Biodiversity and systematics / Plant phylogenetic systematics, Phylogeography

Academic & Professional Experience

  • 2020/04 - Today Hokkaido University Field Science Center for Northern Biosphere
  • 2015/04 - 2020/03 Hokkaido University Botanic Garden, Field Science Center for Northern Biosphere Assistant professor
  • 2010/02 - 2015/03 Academia Sinica, Taiwan Biodiversity Research Center Postdoc


  • 2004/04 - 2007/03  University of the Ryukyus  Graduate School of Engineering and Science

Research Activities

Published Papers

    Phytotaxa 543 (1) 1179-3155 2022/04/08 
    We discussed the typification of the name Saxifraga yuparensis applicable to an alpine plant described from Hokkaido, northern Japan. The holotype is not found in the cited herbarium and other herbaria related to Nosaka. No isotypes or paratypes were cited in its protologue, and no other uncited specimens are unambiguously deduced to have been used by Nosaka when describing the species and do not comprise the original material (Art. 9.4 of the Botanical Code). Therefore, an illustration (Fig. 11 in Nosaka 1974) published as part of the protologue is the only original material that can be chosen in lectotype designation in conformity with Art. 9.12. The illustration is here designated as the lectotype for the name.
  • Yan‐Hua Hu, Wen‐Jian Liu, Xiao‐Fei Song, Guo‐Xing Deng, Koh Nakamura, Lei Wu, Quan‐Ru Liu
    Nordic Journal of Botany 39 (6) 0107-055X 2021/06 [Refereed]
    Phytotaxa 494 (1) 151 - 164 1179-3155 2021/03/31 [Refereed]
    Here we describe a natural hybrid of Philippine Begonia from Bulabog Puti-an National Park in Dingle, Iloilo, Panay Island. The hybrid, named Begonia ×dinglensis after its place of origin, grows on moist, coralline-rock slopes at 200 m elevation. Morphological, molecular, and cytological evidence support its origin from natural hybridization between Philippine endemics B. camiguinensis and B. nigritarum.
  • Phylogenetic position of Lagotis kunawurensis (Plantaginaceae) in Himalaya, a species of boreal L. glauca aggregate.
    Koh Nakamura, Rinchen Yangzom, Atsushi Sugano, Yoshinori Murai
    Bulletin National Museum of Nature and Science, Series B, Botany 47 1 - 6 2021/03 [Refereed]
  • K. Nakamura, Y. Shiotania, T. Fukuda, E.A. Marchuk, E.A. Petrunenko, P.V. Krestov, S.N. Bondarchuk, Y. Nishikawa, T. Shimamura, Y. Fujimura
    Phytokeys 170 83 - 91 2020/12 [Refereed]
  • New localities of seed plants recorded from the subtropical Ryukyus of Japan at island level based on herbarium data
    Goro Kokubugata, Atsushi Ebihara, Yukiko Saito, Masaharu Amano, Atsushi Abe, Koh Nakamura, Akiyo Naiki, Tadashi Kajita, Masatsugu Yokota
    Bulletin National Museum of Nature and Science, Series B, Botany 46 75 - 87 2020/05 [Refereed]
  • The first record of the genus Vitex (Lamiaceae) from Hokkaido, northern Japan
    Koh Nakamura, Goro Kokubugata, Ken Sato
    Journal of Phytogeography and Taxonomy 68 2020 [Refereed][Not invited]
  • Genetic diversity and population structure of Lychnis wilfordii (Caryophyllaceae) with newly developed 17 microsatellite markers
    Bora Kim, Koh Nakamura, Saya Tamura, Byoung Yoon Lee, Myounghai Kwak
    Genes & Genomics 2019 [Refereed][Not invited]
  • 崕山固有の希少植物キリギシソウの保全における今後の課題:基亜種カラフトミヤマイチゲにみる健全な生育環境と,キリギシソウの生息域外保全
    Koh Nakamura
    崕山自然保護20周年記念誌 26 - 33 2019 [Not refereed][Invited]
  • 北海道大学植物園ウェブサイトのリニューアル:一般向けサイト,研究・教育者向けサイト,英語サイトの作成
    板羽貴史, 高田純子, 中村剛, 加藤克
    北大植物園技術報告・年次報告 17 2 - 4 2019 [Not refereed][Not invited]
  • Reappraisal of Tashiroea as a genus independent of Bredia (Melastomataceae) based on molecular data
    Goro Kokubugata, Koh Nakamura, Wen-Hsi Kuo, Zhe-Chen Qi, Kuo-Fang Chung, Cheng-Xin Fu, Yumiko Suzuki, Masatsugu Yokota
    Phytotaxa 392 75 - 83 2019 [Refereed][Not invited]
  • Saya Tamura, Tomoko Fukuda, Elena A. Pimenova, Ekaterina A. Petrunenko, Pavel V. Krestov, Svetlana N. Bondarchuk, Olga A. Chernyagina, Yoshihisa Suyama, Yoshihiro Tsunamoto, Ayumu Matsuo, Hayato Tsuboi, Hideki Takahashi, K. E.N. Sato, Yoko Nishikawa, Takashi Shimamura, Hiroko Fujita, K. O.H. Nakamura
    Phytotaxa 373 (1) 53 - 70 1179-3155 2018/10/23 [Refereed][Not invited]
    © 2018 Magnolia Press. An alpine plant Saxifraga yuparensis is endemic to a scree consisting of greenschist of Mt. Yubari in Hokkaido, Japan and it has been proposed as an immediate hybrid derived from two species of the same section Bronchiales based on morphological intermediacy: namely S. nishidae, a diploid species endemic to a nearby cliff composed of greenschist and tetraploid S. rebunshirensis comparatively broadly distributed in Japan and Russian Far East. Saxifraga yuparensis is red-listed and it is crucial for conservation planning to clarify whether this is an immediate hybrid and lacks a unique gene pool. The immediate-hybrid hypothesis was tested by molecular and cytological data. In nuclear ribosomal and chloroplast DNA trees based on maximum parsimony and Bayesian criteria, S. yuparensis and S. rebunshirensis formed a clade with several other congeners while S. nishidae formed another distinct clade. Genome-wide SNP data clearly separated these three species in principal coordinate space, placing S. yuparensis not in-between of S. rebunshirensis and S. nishidae. Chromosome observation indicated that S. yuparensis is tetraploid, not triploid directly derived from diploid-tetraploid crossing. Additionally, observation of herbarium specimens revealed that leaf apex shape of S. yuparensis fell within the variation of S. rebunshirensis. These results indicate that S. yuparensis is not an immediate hybrid of S. rebunshirensis and S. nishidae but a distinct lineage and an extremely narrow endemic species, that deserves for intensive conservation.
  • 植物園と地権者企業、行政が協力した絶滅危惧植物の植え戻し計画と実施の検討:北海道におけるエンビセンノウ(ナデシコ科)の事例
    田村紗彩, 冨士田裕子, 西川洋子, 島村崇志, 稲川博紀, 高田純子, 永谷工, 中村剛
    日本植物園協会誌 (53) 27 - 34 2018 [Refereed][Not invited]
  • 植物園と地権者企業,行政が協力した絶滅危惧植物の植え戻し計画と実施の検討:北海道におけるエンビセンノウ(ナデシコ科)の事例
    田村紗彩, 冨士田裕子, 西川洋子, 島村崇志, 稲川博紀, 高田純子, 永谷工, 中村剛
    日本植物園協会誌 53 1 - 8 2018 [Refereed][Not invited]
  • 北海道指定希少野生植物エンビセンノウ(ナデシコ科)の北大植物園における生態展示の実施
    田村紗彩, 高田純子, 稲川博紀, 永谷工, 冨士田裕子, 中村剛
    北大植物園技術報告・年次報告 16 11 - 17 2018 [Refereed][Not invited]
  • 「琉球の植物」データベース
    琉球の植物研究グループ(阿部篤志, 海老原 淳, 國府方吾郎, 齊藤由紀子, 中村剛, 横田昌嗣 2018 [Not refereed][Not invited]
  • Tsukasa Iwashina, Goro Kokubugata, Koh Nakamura, Takayuki Mizuno, Hari Prasad Devkota, Masatsugu Yokota, Yoshinori Murai, Yukiko Saito
    Natural Product Communications 13 (12) 1641 - 1644 1934-578X 2018 [Refereed][Not invited]
    Fourteen flavonols, four flavones and six isoflavones were isolated from the aerial parts of two Japanese Glycine species, G. tabacina and G. koidzumii, and the leaves of Taiwanese G. max subsp. formosana. Of their flavonoids, twelve flavonols were identified as kaempferol 3-O-sophoroside (1), 3-O-rutinoside (2), 3-O-robinobioside (3) and 3-O-rhamnosyl-(1→4)-[rhamnosyl-(1→6)-galactoside] (4), quercetin 3-O-gentiobioside (5), 3-O-glucoside (6), 3-O-galactoside (7), 3-O-rutinoside (8), 3-O-robinobioside (9) and 3-O-rhamnosyl-(1→4)-[rhamnosyl-(1→6)-galactoside] (10), and isorhamnetin 3-O-rutinoside (11) and 3-O-robinobioside (12). Other two flavonols were characterized as isorhamnetin 3-O-rhamnosylrhamnosylglucoside (13) and 3-O-rhamnosylrhamnosylgalactoside (14). Four flavones and six isoflavones were estimated as schaftoside (15), apigenin 6,8-di-C-arabinoside (16), luteolin 7-O-glucoside (17) and chrysoeriol 7-O-glucoside (18), and daidzein 7-O-glucoside (19), 4´-O-glucoside (20) and 7-O-xylosylglucoside (21), genistein 7-O-glucoside (22) and 4´-O-glucoside (23), and 3´-O-methylorobol 7-O-glucoside (24). Although flavonoid composition of G. tabacina and G. koidzumii was similar to each other, that of G. max subsp. formosana was different with those of two Japanese Glycine species described above. Flavonoids of their Glycine species were reported for the first time except for those of G. tabacina.
  • Takuro Ito, Chih-Chieh Yu, Koh Nakamura, Kuo-Fang Chung, Qin-er Yang, Cheng-Xin Fu, Zhe-Chen Qi, Goro Kokubugata
    MOLECULAR PHYLOGENETICS AND EVOLUTION 113 9 - 22 1055-7903 2017/08 [Refereed][Not invited]
    We explored the temporal and spatial diversification of the plant genus Sedum L. (Crassulaceae) in Taiwan based on molecular analysis of nrITS and cpDNA sequences from East Asian Sedum members. Our phylogenetic and ancestral area reconstruction analysis showed that Taiwanese Sedum comprised two lineages that independently migrated from Japan and Eastern China. Furthermore, the genetic distances among species in these two clades were smaller than those of other East Asian Sedum clades, and the Taiwanese members of each Glade occupy extremely varied habitats with similar niches in high-mountain regions. These data indicate that species diversification occurred in parallel in the two Taiwanese Sedum lineages, and that these parallel radiations could have occurred within the small continental island of Taiwan. Moreover, the estimated time of divergence for Taiwanese Sedum indicates that the two radiations might have been correlated to the formation of mountains in Taiwan during the early Pleistocene. We suggest that these parallel radiations may be attributable to the geographical dynamics of Taiwan and specific biological features of Sedum that allow them to adapt to new ecological niches. (C) 2017 Elsevier Inc. All rights reserved.
  • 北海道の自然を特徴づける湿地植物の保全遺伝学的研究
    中村剛, 田村紗彩
    公益財団法人栗林育英学術財団 平成27年度研究助成報告書 2016 [Not refereed][Not invited]
  • Saya Tamura, Hiroko Fujita, Yoko Nishikawa, Takashi Shimamura, Hironori Inagawa, Junko Takada, Koh Nakamura
    Bulletin of Japan Association of Botanical Gardens 日本植物園協会 51 (51) 33 - 43 0389-5246 2016 [Refereed][Not invited]
  • Lu-Yao Chen, Ya-Nan Cao, Na Yuan, Koh Nakamura, Guo-Ming Wang, Ying-Xiong Qiu
    MOLECULAR BREEDING 35 (9) e187  1380-3743 2015/09 [Refereed][Not invited]
    Neolitsea sericea (Lauraceae), endemic to East Asian land-bridge islands, is an economically important tree species because of its characteristic aroma and timber uses. However, due to the lack of efficient molecular markers, the genetic diversity and historical demography of this endemic species is not clearly understood. In this study, we performed high-throughput transcriptome sequencing of N. sericea leaves using the Illumina HiSeq (TM) 2000 sequencing platform, and generated large transcript sequences for functional characterization and development of gene-associated SSR markers. A total of 68,624 unigenes (mean length 733 bp) were assembled from about 54.7 million reads, and 41,130 (59.94 %) unigenes of all the assembled unigenes showed similarity to public databases. From 68,624 unigenes, 13,213 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified. Di-nucleotide SSRs were the most abundant motif (36.5 %), followed bymono-(32.3 %) and tri-nucleotide (26.5 %) repeats. From the 13,213 EST-SSRs, 1191 primer pairs were designed for marker mining. After selecting 131 of these pairs at random for further validation, 13 polymorphic pairs were identified as polymorphic SSR loci. These 13 EST-SSR markers showed intermediate levels of genetic diversity (e.g., N-A = 7.15; mean H-E = 0.51) when surveyed across six populations from East China (2), Taiwan (1), Korea (1), and the Ryukyus (1) and Honshu (1) of Japan. Both genetic distance and STRUCTURE analyses identified two genetic clusters largely congruent with recent findings revealed by variations in chloroplast DNA sequences and genomic SSRs. The EST-SSR markers developed in our research will be an information resource for future studies on ecological, evolutionary, and conservation genomics in N. sericea.
  • Goro Kokubugata, Hidetoshi Kato, Duilio Iamonico, Hana Umemoto, Takuro Ito, Koh Nakamura, Noriaki Murakami, Masatsugu Yokota
    PHYTOTAXA 217 (3) 279 - 287 1179-3155 2015/06 [Refereed][Not invited]
    Molecular phylogenetic analyses, morphological observations, and nomenclatural studies were carried out to investigate the taxonomic status of Portulaca boninensis, endemic species from the Bonin (Ogasawara) Islands (Japan). The results addressed controversy between the widely naturalized P. boninensis and P. pilosa, indicating that they are phylogenetically and morphologically distinct. Furthermore, P. boninensis was showed to be conspecific to P. psammotropha which is until now recorded in southern China, Taiwan, and the northern Philippines, but not in the Ryukyus. The name of P. psammotropha was lectotypified on a specimen preserved at K. Based on phylogeography, P. psammotropha likely migrated to the Oceanic Bonin Islands oversea by sea-current dispersal or by exo-and/or end ozoochory through migratory birds without passing through Ryukyus.
  • Kenta Watanabe, T. Y. Aleck Yang, Chihiro Nishihara, Tai-Liang Huang, Koh Nakamura, Ching-I Peng, Takashi Sugawara
    BOTANICAL STUDIES 56 e10  1999-3110 2015/05 [Refereed][Not invited]
    Background: Psychotria cephalophora Merr. (Rubiaceae), a shrub in oceanic islands of Taiwan and the Philippines, appears to be distylous, but distyly is usually rare on oceanic islands. To elucidate the functional breeding system of P. cephalophora can improve our understanding of plant reproductive ecology on oceanic islands. Results: Field investigations on Lanyu (Orchid Island) off the coast of southeastern Taiwan revealed the flowers to be distylous with short (S)-and long (L)-styled morphs, with only one morph per individual. Laboratory observations revealed that both morphs had stainable pollen grains and indicated dimorphism in stigmatic papillae and pollen size. In hand pollination experiments, the pollen tubes reached the base of the style in intermorph crossing, whereas they rarely penetrated stylar tissue in intramorph crossing and selfing. Open pollinated S- and L-styled flowers produced fruit. Conclusions: The results indicate that the breeding system of P. cephalophora is morphologically and functionally distylous.
  • Koh Nakamura, Tetsuo Denda, Goro Kokubugata, Chiun-Jr Huang, Ching-I Peng, Masatsugu Yokota
    PLANT SYSTEMATICS AND EVOLUTION 301 (1) 337 - 351 0378-2697 2015/01 [Refereed][Not invited]
    In continental island biogeography, geologically age-old straits have been considered to be the most likely barriers in determining geographical patterns of speciation/genetic differentiation among islands. Straits with similar ages may have had different influences if geographical width across the straits had fluctuated differently in the past. However, this issue has seldom been discussed. We explored it by studying the Viola iwagawaetashiroi species complex in the Ryukyu Archipelago, Japan. The archipelago is divided into three island groups, the northern, central, and southern Ryukyus, by two old straits called the Tokara and Kerama gaps, which are roughly of the same age. Bayesian and maximum parsimony phylogenetic analyses of section Plagiostigma and Bayesian molecular dating using multiple calibration points were conducted based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences. To reveal the detailed genealogy of the species complex, statistical parsimony networks were estimated separately for the ITS and chloroplast DNA (cpDNA) sequences and a calibrated multispecies coalescent tree based on both ITS and cpDNA sequences was constructed. Results suggest that the V. iwagawae-tashiroi species complex originated in the Ryukyu Archipelago when this region formed part of the East Asian continental margin or was formed by a few larger islands and that the complex was already distributed across the archipelago by the late Pliocene-early Pleistocene. Divergence time estimations suggest that the Kerama Gap has been a long-term effective barrier to dispersal preventing gene flow across it, whereas recent dispersal over the Tokara Gap was inferred. These contrasting results are likely explained by the fact that the minimum geographical width across the straits is geohistorically and currently greater over the Kerama Gap than at the Tokara Gap.
  • Koh Nakamura, Yi-Fu Wang, Meng-Jung Ho, Kuo-Fang Chung, Ching-I Peng
    Taiwania 60 49 - 53 2015 [Refereed][Not invited]
  • Koh Nakamura, Shih-Wen Chung, Yoshiko Kono, Meng-Jung Ho, Tian-Chuan Hsu, Ching-I Peng
    PLOS ONE 9 (10) e109797  1932-6203 2014/10 [Refereed][Not invited]
    A new species Ixeridium calcicola (Compositae) endemic to middle altitude (ca 1,000-2,000 m asl) limestone mountains of eastcentral Taiwan is described based on morphological and chromosome cytological observations and molecular phylogenetic analyses. Ixeridium calcicola resembles Ixeridium transnokoense, endemic to upper montane and alpine ranges (2,600-3,500 m asl) of Taiwan, in the dwarf habit, but differs in the oblong to lanceolate leaf blades (vs. linear to linear-lanceolate), the presence of mucronulate teeth on the leaf margin and petiole (vs. smooth to very sparse), the dark purple lower leaf surface (vs. greenish), the capitulum with 10 to 12 florets (vs. 5 to 7) and 8 to 10 inner phyllaries (vs. 5, rarely to 7). The basic chromosome number in Ixeridium was known as X = 7. However, the new species has a basic chromosome number of X = 8, as recorded also in the closely related Ixeris. Molecular phylogenetic analyses with the expanded sampling of Ixeridium and Ixeris including both type species supported the monophyly of each of the genera and the placement of the new species in Ixeridium. The result of the phylogenetic analyses and detailed observation of the chromosome morphology revealed that X = 8 in Ixeridium calcicola is derived from centric fission in an ancestral karyomorphotype with X = 7 in Ixeridium. Ixeridium calcicola and Ixeridium transnokoense formed a Taiwan endemic lineage and their estimated divergence time was in the middle Pleistocene. Their common ancestral lineage may have experienced altitudinal distribution shifts in response to glacial-interglacial temperature fluctuation, and a lineage which had not retreated to alpine ranges in an interglacial period likely survived in a limestone refugium, where ordinary plant species did not grow, leading to allopatric speciation.
  • Takuro Ito, Koh Nakamura, Chan-Ho Park, Gwan-Pil Song, Ayako Maeda, Yuki Tanabe, Goro Kokubugata
    PHYTOTAXA 177 (4) 221 - 230 1179-3155 2014/09 [Refereed][Not invited]
    Our molecular phylogeographic analyses based on the nrDNA ITS and cpDNA trnLF of Sedum tosaense populations in the Shikoku District, Japan and Jeju Island, Korea suggested a disjunct distribution. Plants of S. tosaense from the two regions comprised a well-supported clade consisted of plants from Kochi (Shikoku District) and those from Jeju Island; we estimated a divergence time of 0.61 Ma between the Kochi and Jeju populations based on the ITS and partial trnLF. We conclude that: 1) S. tosaense has a disjunct distribution between Kochi and Jeju Island, and 2) plants of this species might have dispersed between Kochi and Jeju Island over water, but not via a land bridge, which flooded before subclade divergence.
  • Koh Nakamura, Meng-Jung Ho, Chia-Jou Ma, Hsun-An Yang, Ching-I Peng
    CONSERVATION GENETICS RESOURCES 6 (3) 649 - 651 1877-7252 2014/09 [Refereed][Not invited]
    In East and Southeast Asian islands, forest area is decreasing and population size of multiple Ophiorrhiza species (Rubiaceae) is diminishing. Here we report the first expressed sequence tag-derived microsatellite markers, which can be applied to wide range of species of the genus. We developed 38 tri- and tetra-nucleotide microsatellite markers based on nonredundant unigenes of O. pumila and tested polymorphism of nine markers using the phylogenetically distant congener O. japonica (n = 96). The number of alleles ranged from 4 to 9. Observed and expected heterozygosities ranged 0.044-0.631 and 0.096-0.674, respectively. The polymorphic information content ranged 0.094-0.626. No null allele, significant deviation from Hardy-Weinberg equilibrium, or significant linkage disequilibrium was observed. Additional tests of cross-species amplification with three other congeners were successful in the nine markers. These markers will be used to investigate genetic diversity and differentiation of island populations of multiple Ophiorrhiza species to build conservation plans.
  • Bo Ding, Koh Nakamura, Yoshiko Kono, Meng-Jung Ho, Ching-I Peng
    BOTANICAL STUDIES 55 e62  1999-3110 2014/08 [Refereed][Not invited]
    Background: Continental China is the center of Begonia species diversity in Asia and contains more than 60 species out of about 110 named species of section Platycentrum. Mt. Jinyun, located in Chongqing City at the upper reaches of the Yangtze River, harbors a subtropical broadleaved forest with high species diversity. During a botanical survey in Mt. Jinyun, an unknown Begonia species of sect. Platycentrum with palmately compound leaves was collected and studied based on detailed morphological observations and cytological and molecular phylogenetic analyses. Results: The unknown Begonia bears a superficial resemblance to B. hemsleyana in having palmately compound leaves, a feature unseen in other species of sect. Platycentrum in China. It is however sharply distinct from the latter in the acaulous habit with aerial stems seen only at anthesis and long rhizomes (vs. erect stems to 70 cm or taller with short rhizomes), 4-6 pinnatilobed leaflets with indistinct, decurrent petiolules (vs. 7-10 serrate leaflets with distinct petiolules), and white (vs. pink) tepals. Molecular phylogenetic analyses based on nuclear ribosomal DNA and chloroplast DNA sequences indicated that this species was allied to Platycentrum species occurring in Southwest and South-central China and Vietnam, including B. hemsleyana, and clearly separable from these species. Somatic chromosome number of 2n = 22 was reported for this unknown species. The diploid chromosome number is agreeable with those published for Begonia sect. Platycentrum. Conclusions: The unknown Begonia is confirmed to be a new species of sect. Platycentrum and hereto described as Begonia jinyunensis C.-I Peng, B. Ding & Q. Wang.
  • Yun-Rui Mao, Yong-Hua Zhang, Koh Nakamura, Bi-Cai Guan, Ying-Xiong Qiu
    JOURNAL OF SYSTEMATICS AND EVOLUTION 52 (4) 487 - 499 1674-4918 2014/07 [Refereed][Not invited]
    Species of Podophyllum, Dysosma, Sinopodophyllum, and Diphylleia, genera from Podophylloideae of Berberidaceae, have long been used in traditional herbal medicine in East Asia and/or North America. Accurate identification of the species of these four genera is crucial to their medicinal uses. In this study, we tested the utility of nine barcodes (matK, rbcL, atpH-atpI, rpl32-trnL(UAG), rps18-clpp, trnL-trnF, trnL-ndhJ, trnS-trnfM, and internal transcribed spacer (ITS)) to discriminate different species of Podophylloideae. Thirty-six individuals representing 12 species of Podophylloideae were collected from different locations in China, Japan, and North America. We assessed the feasibility of amplification and sequencing of all markers, examined the levels of the barcoding gap based onDNA sequence divergence between ranges of intra-and interspecific variation using pairwise distances, and further evaluated successful identifications using each barcode by similarity-based and tree-based methods. Results showed that nine barcodes, except rps18-clpp, have a high level of primer universality and sequencing success. As a single barcode, ITS has the most variable sites, greater intra-and interspecific divergences, and the highest species discrimination rate (83%), followed by matK which has moderate variation and also high species discrimination rates. However, these species can also be discriminated by ITS alone, except Dysosma versipellis (Hance) M. Cheng ex T. S. Ying and D. pleiantha (Hance) Woodson. The combination of ITS+matK did not improve species resolution over ITS alone. Thus, we propose that ITS may be used as a sole region for identification of most species in Podophylloideae. The failure of ITS to distinguish D. versipellis and D. pleiantha is likely attributed to incomplete lineage sorting due to recent divergence of the two species.
  • Koh Nakamura, Chia-Jou Ma, Chiun-Jr Huang, Meng-Jung Ho, Hsun-An Yang, Ching-I Peng
    CONSERVATION GENETICS RESOURCES 6 (2) 447 - 449 1877-7252 2014/06 [Refereed][Not invited]
    Ophiorrhiza japonica (Rubiaceae) in Taiwan shows altitudinal morphological differentiation, suggesting altitudinal genetic differentiation. However, global warming and/or road building are possibly causing human-mediated altitudinal gene flow and genetic disturbance. To investigate this possibility, we developed the first nuclear microsatellite markers for the genus. Using the low-cost compound microsatellite marker technique, 17 markers were developed and nine markers were polymorphic. The number of alleles per polymorphic locus ranged from 2 to 13. At population level, observed (H (o) ) and expected (H (e) ) heterozygosities ranged 0.070-0.831 and 0.068-0.812, respectively. The polymorphic information content ranged 0.066-0.787. No null allele, significant deviation from Hardy-Weinberg equilibrium, or significant linkage disequilibrium was observed. The 17 marker loci were successfully PCR-amplified in three congeneric species except for three cases. The developed microsatellite markers will be used to investigate genetic structure and gene flow among O. japonica populations at different altitudes.
  • Koh Nakamura, Goro Kokubugata, Rosario Rivera Rubite, Chiun-Jr Huang, Yoshiko Kono, Hsun-An Yang, Auriea Lopez-Feliciano, Mina L. Labuguen, Masatsugu Yokota, Ching-I Peng
    BOTANICAL JOURNAL OF THE LINNEAN SOCIETY 174 (3) 305 - 325 0024-4074 2014/03 [Refereed][Not invited]
    Equatorward contraction and re-expansion during and after the last glacial maximum has been reported for temperate plants, but little is known about latitudinal shifts of tropical plants in insular Asia. We used molecular methods to test the post-glacial migration hypothesis for Begonia fenicis at the northern limit of tropical insular Asia, namely, the northern Philippines, southern Taiwan and the southern Ryukyus of Japan. Based on internal transcribed spacer sequences, analyses of phylogeographical structure suggested long-term survival of island populations and negated recent northward migration; demographic analyses indicated spatial expansion in the early Pleistocene and subsequent stable demography. Based on nuclear microsatellites, Bayesian clustering and other spatial analyses indicated inter-island differentiation, and coalescent analysis of migration indicated the lack of inter-island migration during and after the last glacial maximum. Our results refuted the postglacial migration hypothesis for B. fenicis and suggest in situ survival through the last glacial maximum. The stable historical distribution and demography are probably attributable to the Kuroshio Current bringing warm and humid air, which washed these islands even during the glacial periods. Additionally, because these are low islands, absence of competition with montane plants descending to the lowlands during cooler periods may have mitigated the influence of temperature lowering and facilitated their survival. (c) 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 305-325.
  • Goro Kokubugata, Koh Nakamura, Yukiko Saito, Mina L. Labuguen, Auriea Lopez-Feliciano, Masatsugu Yokota
    Bulletin of the National Museum of Nature and Science. Series B, Botany National Museum of Nature and Science 40 (1) 47 - 53 1881-9060 2014 [Refereed][Not invited]
  • Hana Umemoto, Koh Nakamura, Akiko Maeda, Masatsugu Yokota, Goro Kokubugata
    Bulletin of the National Museum of Nature and Science. Series B, Botany National Museum of Nature and Science 40 (4) 153 - 161 1881-9060 2014 [Refereed][Not invited]
  • Koh Nakamura, Rosario Rivera Rubite, Goro Kokubugata, Yoshiko Kono, Masatsugu Yokota, Ching-I Peng
    PHYTOTAXA 152 (1) 56 - 58 1179-3155 2013/12 [Refereed][Not invited]
  • Koh Nakamura, Rosario Rivera Rubite, Yoshiko Kono, John Rey Callado, Ching-I Peng
    PHYTOTAXA 145 (1) 27 - 37 1179-3155 2013/11 [Refereed][Not invited]
    We describe Begonia tandangii, a new species of Begonia sect. Baryandra from the Sierra Madre Mountain Range of Luzon Island, the Philippines. Begonia tandangii has a close resemblance to B. fenicis in gross morphology, differing in having leaf margin sparsely fringed with minute hairs (vs. glabrous or with minute hairs only on teeth) and capsules with broadly-ovate outline and an acuminate apex (vs. capsules with broadly-obovate outline and a rounded to truncate apex). Phylogenetic analyses of Philippines species of sect. Baryandra based on ITS sequences revealed that B. tandangii was clearly separated from B. fenicis. Begonia tandangii is currently known only from the type locality in a coastal forest of Baler, Aurora Province, which is in the neighborhood of Aurora Memorial National Park.
  • Goro Kokubugata, Koh Nakamura, Yumiko Hirayama, Masatsugu Yokota
    PHYTOTAXA 117 (1) 11 - 22 1179-3155 2013/07 [Refereed][Not invited]
    We used molecular phylogenetic and morphological data to reexamine the taxonomic status of Portulaca okinawensis (equivalent to P. pilosa subsp. okinawensis) endemic to the central Ryukyu islands, southwestern Japan. Our molecular analyses showed that P. okinawensis is monophyletic, sister to the clade of P. psammotropha and P. tuberosa and it is not closely related to P. pilosa subsp. pilosa. Two subclades, one comprising plants from the Okinawa Islands and the other from the Amami Islands, were recognized. The plants from the Okinawa Islands had more than 20 stamens, orange-yellow nallowly obovate to oblanceolate petals, and reddish-green stems (as the holotype), while the plants from the Amami Islands had less than 20 stamens, lemon-colored obovate petals, and bright-green stems. The molecular and morphological data support a taxonomic treatment of Walker & Tawada (1951) regarding P. okinawensis as a separate species, also suggesting that the plants from the Amami and Okinawa islands should be treated as different taxa. A new variety Portulaca okinawensis var. amamiensis was here described.
  • Koh Nakamura, Yoshiko Kono, Chiun-Jr Huang, Kuo-Fang Chung, Ching-I Peng
    SYSTEMATIC BOTANY 38 (2) 507 - 516 0363-6445 2013/04 [Refereed][Not invited]
    Youngia japonica, the type species for its genus, has the widest distribution in the genus and is invasive worldwide. Recent molecular phylogenetic analysis supported recognition of three ecologically differentiated entities: Y. japonica subsp. formosana, Y. japonica subsp. japonica, and an undescribed morphological variant thought to be a new subspecies in Taiwan. These are the only infraspecific taxa currently recognized in this morphologically variable species. Use of proper names for these taxa and related species is important for future revision of Y. japonica in other regions, for nomenclature and biogeography of the genus, and for activities to control its invasiveness. Careful examination of the holotype of Y. japonica subsp. formosana and relevant literature revealed that the name has long been misapplied to Youngia in mountain ranges in Taiwan; it should be applied to the morphological variant growing on littoral, raised coral reefs in southwestern Taiwan. The misidentified entity is here described as Youngia japonica subsp. monticola. In addition, Y. taiwaniana was treated as a synonym of Y. longiflora (equivalent to Y. japonica subsp. longiflora) in the Flora of Taiwan, but the holotype has achenes with a long beak and does not belong to Youngia. It is here treated as a synonym of Ixeridium laevigatum. A key to Youngia in Taiwan is provided.
  • Goro Kokubugata, Yukiko Saito, Koh Nakamura, Auriea Lopez-Feliciano, Mina L. Labuguen, Masatsugu Yokota
    Bulletin of the National Museum of Nature and Science. Series B, Botany National Museum of Nature and Science 39 (2) 95 - 100 1881-9060 2013 [Refereed][Not invited]
  • Nakamura K, Denda T, Kokubugata G, Forster PI, Wilson G, Peng CI, Yokota M
    Biological Journal of the Linnean Society 105 (1) 197 - 217 1095-8312 2012/12 [Refereed][Not invited]
    An antitropical distribution represents an intriguing disjunction, in which a given species or sister lineages occupy regions north and south of the tropics but are absent from the intervening areas. Solenogyne mikadoi endemic to the Ryukyu Archipelago is regarded as an Australian element. Testing the phylogenetic relationship with Australian congeners and discussing the onset timing and causes of the disjunction would potentially enhance the understanding of antitropical distribution. A nuclear ribosomal DNA phylogeny was reconstructed using Bayesian and most parsimonious criteria with allied genera. Solenogyne was monophyletic and clustered with Lagenophora huegelii endemic to Australia, indicating the antitropical distribution and Australian origin of Solenogyne. Multispecies coalescent analysis based on nuclear ribosomal DNA and chloroplast DNA indicated the divergence of S. mikadoi and Australian congeners in the Plio-Pleistocene. Phylogenetic network analyses suggested that the ancestral lineage of S. mikadoi first colonized the southernmost island in the archipelago and then dispersed northward. The migration to the archipelago likely followed the flourishing of Solenogyne in open vegetation communities that radiated in south-eastern Australia during the late Pliocene. This disjunction might arise through long-distance dispersal across the tropics or, alternatively, through extinction in the tropics as a result of unsuitably high temperatures during climate oscillation and/or competitions from diverse tropical flora surviving since the early Tertiary. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 197217.
  • Goro Kokubugata, Koh Nakamura, Paul I. Forster, Gary W. Wilson, Ailsa E. Holland, Yumiko Hirayama, Masatsugu Yokota
    AUSTRALIAN SYSTEMATIC BOTANY 25 (5) 364 - 373 1030-1887 2012/10 [Refereed][Not invited]
    Morphological comparisons and molecular phylogenetic analyses were conducted to resolve taxonomic confusion in Cassytha glabella and C. pubescens, both of which were first described from Australia and subsequently considered to be disjunctly distributed between Australia and the Ryukyu Archipelago of Japan. In the morphological comparisons, plants considered as C. pubescens in the Ryukyus differ from C. pubescens in Australia in the presence or absence of hairs on the petals, and those considered as C. glabella in the Ryukyus differ from the C. glabella in Australia in bract and peduncle morphology. The molecular analyses indicated that plants attributed to C. pubescens in the Ryukyus were not closely related to C. pubescens in Australia, and were nested in a clade of populations of a Pan-Western Pacific species C. filiformis. Plants attributed to C. glabella in the Ryukyus were distantly related to C. glabella in Australia. We concluded that plants considered as C. pubescens and C. glabella in the Ryukyus are to be respectively treated as C. filiformis and the Ryukyu endemic species C. pergracilis.
  • Sheng-Nan Zhai, Hans Peter Comes, Koh Nakamura, Hai-Fei Yan, Ying-Xiong Qiu
    JOURNAL OF BIOGEOGRAPHY 39 (7) 1347 - 1360 0305-0270 2012/07 [Refereed][Not invited]
    Aim Our goals were: (1) to assess the population genetic structure and demographic divergence history of a bird-dispersed tree, Neolitsea sericea, endemic to East Asian land-bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc. Location JapanRyukyuTaiwan Island Arc and Chinese/Korean offshore islands. Methods We applied 10 nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker (psbAtrnH intergenic spacer) to 31 populations (397 and 326 individuals, respectively) from throughout the species range to infer current patterns of genetic diversity and structure, and pollen-to-seed migration ratios (r). A coalescent-based isolation-with-migration (IM) model was applied to the combined nSSR/cpDNA data set to estimate lineage divergence times and population demographic parameters. Results The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the Tokara Gap, a narrow (c. 37 km wide) but deep (> 1000 m) sea-strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages to c. 0.07 Ma (90% highest posterior density interval: 0.020.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post-divergence gene flow between them. Main conclusions The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an ancient sea-barrier hypothesis for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence of N. sericea, including not only land-bridge submergence, but also island configuration, and/or constraints on adaptation along a latitudinal temperature gradient.
  • Koh Nakamura, Kuo-Fang Chung, Chiun-Jr Huang, Yoshiko Kono, Goro Kokubugata, Ching-I Peng
    MOLECULAR PHYLOGENETICS AND EVOLUTION 63 (2) 486 - 499 1055-7903 2012/05 [Refereed][Not invited]
    Weeds with broad distributions and large morphological variation are challenging for systematists and evolutionarily intriguing because their intensive dispersal would likely prevent local morphological differentiation. Study on weeds will help to understand divergence in plants unlikely to be affected by geographical and ecological barriers. We studied Youngia japonica based on nrDNA and cpDNA sequences. This is a widespread native in Asia and invasive worldwide: nevertheless, three subspecies (japonica, longiflora, and formosana) and an undescribed variant occur in Taiwan. Bayesian and the most parsimonious phylogenies revealed that subspecies longiflora is a different linage and independently arrived in Taiwan during the Pleistocene via land connection to the Asian Continent. Bayesian time estimation suggested that Youngia in Taiwan diverged in the lower Pleistocene or more recently. Extreme habitats that emerged in the Pleistocene, i.e., cold mountain ranges for subspecies formosana and xeric, raised coral reefs for the undescribed Youngia variant probably had triggered the divergence. Components of Youngia in Taiwan are not monophyletic; a coalescent-based test suggested incomplete lineage sorting. Nevertheless, the samples within each taxon share unique morphological features suggesting a common gene pool and each taxon has different dominant ITS and/or cpDNA types; these conditions suggest ongoing process toward monophyly via coalescent processes and support the delimitation of intraspecific taxa. (C) 2012 Elsevier Inc. All rights reserved.
  • Na Yuan, Yi Sun, Koh Nakamura, Ying-Xiong Qiu
    AMERICAN JOURNAL OF BOTANY 99 (2) E43 - E45 0002-9122 2012/02 [Refereed][Not invited]
    Premise of the study: Microsatellite primers were developed for a heterostylous herb, Hedyotis chrysotricha to investigate the effect of habitat fragmentation on its genetic diversity and population structure. Methods and Results: Twelve primer sets were developed and their polymorphisms were tested on 47 individuals from two island populations of H. chrysotricha in Thousand Island Lake of China. The number of alleles per locus ranged from five to 10, with an average of seven alleles. Expected heterozygosity per locus ranged from 0.284 to 0.821 and observed heterozygosity ranged from 0.191 to 0.851. Conclusions: We showed that all of the 12 microsatellite markers developed for H. chrysotricha are polymorphic within populations, which should provide a powerful tool for assessing population structure and genetic diversity across fragmented and continuous populations, and for studying the genetic effects of habitat fragmentation on this species.
  • Goro Kokubugata, Koh Nakamura, Paul I. Forster, Yumiko Hirayama, Masatsugu Yokota
    AUSTRALIAN JOURNAL OF BOTANY 60 (5) 417 - 428 0067-1924 2012 [Refereed][Not invited]
    We tested the antitropical distribution of Lobelia loochooensis, endemic to the Ryukyu Archipelago of Japan, and its putative sister species of the same section Hypsela in Oceania (Australia and New Zealand). Molecular phylogenetic analyses based on cpDNA sequences were conducted for 41 Lobelia species of 11 sections including all the species of sect. Hypsela investigated in Asia and Malesia and 32 species of 16 allied genera of family Campanulaceae, because the genus Lobelia is known to be polyphyletic. In the result, L. loochooensis and an Australian endemic L. fluviatilis formed a clade, and this clade was sister to a clade of four New Zealand endemics: L. carens, L. fatiscens, L. fugax and L. ionantha. These two clades were nested in a clade with two other Australian congeners. We conclude that: (1) the lineage of L. loochooensis and the five Lobelia species occurring in Oceania demonstrate an antitropical distribution pattern; and (2) L. loochooensis has likely originated from a dispersal event from Australia to the Ryukyu Archipelago.
  • Koh Nakamura
    Bunrui, Journal of Japanese Society for Plant Systematics 日本植物分類学会 12 (2) 117 - 139 1346-6852 2012 [Refereed][Invited]
  • Koh Nakamura, Chiun-Jr Huang, Rosario Rivera Rubite, Wai-Chao Leong, Yoshiko Kono, Hsun-An Yang, Ching-I Peng
    AMERICAN JOURNAL OF BOTANY 99 (1) E20 - E23 0002-9122 2012/01 [Refereed][Not invited]
    Premise of the study: We developed compound microsatellite markers for Begonia fenicis, a species endemic to eastern and southeastern Asian islands, to investigate geographical genetic structure. Methods and Results: Using the compound microsatellite marker technique, 21 markers were developed and six polymorphic markers were characterized for samples from four islands in Taiwan and southern Japan. The number of alleles per locus ranged from two to six (mean = 4.33). Observed and expected heterozygosities were 0.125-0.725 (0.383) and 0.498-0.719 (0.641), and polymorphic information content was 0.371-0.664 (0.567). The interspecific transferability of the 21 markers was evaluated for eight species of the section Diploclinium from the Philippines; 15 markers were successfully amplified in one to eight species. Conclusions: These results indicate the utility of the six microsatellite markers in B. fenicis to investigate geographical genetic structure. The transferable markers are potentially useful for other species of the section.
  • The architectural stratification and woody species diversity in subtropical evergreen broadleaf forests along a latitudinal thermal gradient of the Ryukyu Archipelago, Japan
    S. M. Feroz, Rempei Suwa, Koh Nakamura, Akio Hagihara, Masatsugu. Yokota
    Raffles Bulletin of Zoology In press 2011 [Refereed][Not invited]
  • Taxonomic reconsideration and phytogeographic implications for Nertera yamashitae (Rubiaceae), endemic to Amami Island of the Ryukyu Archipelago, Japan
    Goro Kokubugata, Koh Nakamura, Yumiko Hirayama, Ching-I Peng, Masatsugu Yokota
    Bulletin of the National Museum of Nature and Science. Series B, Botany 37 9 - 22 2011 [Refereed][Not invited]
  • The impacts of historical barriers on floristic patterns of plant groups with different dispersal abilities in the Ryukyu Archipelago, Japan
    Koh Nakamura, Rempei Suwa, Tetsuo Denda, Masatsugu Yokota
    Raffles Bulletin of Zoology In press 2011 [Refereed][Not invited]
  • Sheng-Nan Zhai, Xiao-Ling Yan, Koh Nakamura, Misako Mishima, Ying-Xiong Qiu
    AMERICAN JOURNAL OF BOTANY 97 (12) E139 - E141 0002-9122 2010/12 [Refereed][Not invited]
    Premise of the study: The development of compound microsatellite markers was conducted in Neolitsea sericea to investigate genetic diversity and population genetic structure of this endangered insular species. Methods and Results: Using the compound microsatellite marker technique, 10 compound microsatellite markers that were successfully amplified showed polymorphism when assessed in 55 individuals from two populations in East China and Japan. Overall, the number of alleles ranged from 3 to 17, with an average of 7.9 alleles per locus. In addition, these primers could be easily amplified in Neolitsea aurata var. paraciculata and N. aurata var. chekiangensis. Conclusions: The highly polymorphic markers developed and characterized in this study will be useful for population genetic studies of N. sericea.
  • Koh Nakamura, Tetsuo Denda, Goro Kokubugata, Rempei Suwa, T. Y. Aleck Yang, Ching-I Peng, Masatsugu Yokota
    JOURNAL OF BIOGEOGRAPHY 37 (10) 1907 - 1918 0305-0270 2010/10 [Refereed][Not invited]
    Aim Phylogeographical patterns in the Ryukyu Archipelago have been explained primarily by landbridge formation and the opening of two straits in the Pliocene, namely the Tokara and Kerama gaps. These old straits have been considered to be the barriers most likely to determine genetic boundaries. To test this, we conducted a molecular analysis of the herb Ophiorrhiza japonica. We discuss the causes of and processes involved in its phylogeographical structure and explore aspects of island separation other than the duration of the straits to explain genetic boundaries at the gaps. Location Ryukyu Archipelago, Japan. Methods Plants were collected from 40 localities in the archipelago and vicinity. Non-coding regions of chloroplast DNA were sequenced. The genealogical relationships among haplotypes were estimated using a statistical parsimony network. To examine the phylogeographical structure, we compared two parameters of population differentiation, namely G(ST) and N(ST), and conducted correlation analysis of genetic and geographical distances. Genetic boundaries were identified using Monmonier's maximum difference algorithm. To test vicariance-dispersal hypotheses, that is, vicariance after migration via the Pliocene landbridge or over-sea dispersal in the Pleistocene, molecular dating analysis was conducted. Results A statistical parsimony network revealed that the haplotypes from the Ryukyu Archipelago and northwards coalesce to one ancestral haplotype in Taiwan. A clear phylogeographical structure was observed: plants within the same population and populations in geographical proximity were phylogenetically close. A genetic boundary was recognized across the Kerama Gap, but not across the Tokara Gap. Dating analysis suggested that population divergence across the Kerama Gap occurred in the early to late Pleistocene. Main conclusions The statistical parsimony network suggests migration from Taiwan and northward range expansion in the archipelago. Based on the divergence time, over-sea dispersal in the Pleistocene is likely, although migration via a Pliocene landbridge is not totally rejected. Negligible genetic differentiation across the Tokara Gap suggests recent over-sea dispersal, possibly facilitated by the small geographical width of the gap. Conversely, the large genetic differentiation across the Kerama Gap is probably explained by the large geographical distance across it. The past splitting of a landbridge would have had a significant influence on population differentiation after a certain geographical distance was reached.
  • Goro Kokubugata, Koh Nakamura, Wataru Shinohara, Yukiko Saito, Ching-I Peng, Masatsugu Yokota
    MOLECULAR PHYLOGENETICS AND EVOLUTION 54 (2) 657 - 663 1055-7903 2010/02 [Refereed][Not invited]
    Phylogenetic analyses were performed using nrITS variations of eight species including one variety of the genus Lysimachia sect. Nummularla in Japan and Taiwan, with another 34 Lysimachia species and Glaux maritime obtained from a DNA database. Among the four dwarf-leaf taxa in Japan and Taiwan, L. japonica var. minutissima of Japan and two Taiwanese species were placed into two different clades: and L. liukiuensis of Japan, was positioned outside of these two clades. These results suggest that three independent dwarfism events generated the four dwarf-leaf taxa; and that there were likely multiple migration events from China to Japan and Taiwan. (C) 2009 Elsevier Inc. All rights reserved.
  • Koh Nakamura, Rempei Suwa, Tetsuo Denda, Masatsugu Yokota
    JOURNAL OF BIOGEOGRAPHY 36 (5) 919 - 928 0305-0270 2009/05 [Refereed][Not invited]
    Floristic differentiation in the Ryukyu Archipelago has been explained primarily by geohistory, specifically landbridge formation and vicariance at the Tokara and Kerama Gaps, two deep-sea channels through the island arc. This ignores current environmental effects, which may also be important. We therefore tested whether the floristic differentiation pattern is explained primarily by the historical effect of the gaps as barriers, or whether a better understanding of floristic differentiation is achieved when both historical and current environmental factors are incorporated. Ryukyu Archipelago, Japan: an assemblage of continental islands. We compiled a presence-absence matrix of 1815 plant species on 26 islands. Floristic dissimilarity distances between islands were calculated using Simpson's similarity index and analysed using cluster analysis. We also conducted multiple regression on distance matrices (MRM) to examine the significance of the historical factors of the gaps and current environmental factors: geographical distance among islands and differences in island area and maximum elevation. We detected clear patterns of floristic differentiation across the gaps. Using the two gaps as explanatory variables, the MRM showed that both had significant effects on floristic dissimilarity distance. However, when geographical distance was added to the explanatory model, the Kerama Gap effect disappeared. When all five explanatory variables were used, the Tokara Gap and geographical distance had positive effects, but area difference had a negative effect. The Kerama Gap and difference in maximum elevation had no effect. The geographical pattern of floristic differentiation appears to indicate the influence of both gaps. However, the MRM indicates that the floristic differentiation across the Kerama Gap is no more than could be explained solely by geographical distance. Across the Tokara Gap, however, floristic differentiation is larger than geographical distance alone can explain. This additional differentiation is attributable to the effect of the historical barrier. To verify the significance of historical effects of vicariance on island biota, the confounding effects of geographical distance must be considered. The distance decay of floristic similarity and negative effect of area difference on floristic differentiation demonstrate that floristic differentiation is better understood by incorporating both historical and current environmental factors.
  • S. M. Feroz, Min Wu, Sahadev Sharma, Yan Li, Rempei Suwa, Koh Nakamura, Akio Hagihara, Tetsuo Denda, Masatsugu Yokota
    Tropics 18 103 - 114 2009 [Refereed][Not invited]
  • Koh Nakamura, Akiko Sato, Shun Kobayashi, Masako Izawa, Tetsuo Denda, Masatsugu Yokota
    Bunrui, Journal of Japanese Society for Plant Systematics 日本植物分類学会 9 (2) 159 - 165 1346-6852 2009 [Refereed][Not invited]
  • 花冠裂片数の変異に基づくヘツカリンドウ(リンドウ科)の2変種
    中村剛, 國府方吾郎, 傳田哲郎, 横田昌嗣
    植物地理・分類研究 56 (1) 33 - 34 2008 [Not refereed][Not invited]
  • Two forms of Swertia tashiroi (Maxim.) Makino (Gentianaceae) based on variation in the number of corolla lobes
    Koh Nakamura, Goro Kokubugata, Tetsuo Denda, Masatsugu Yokota
    Journal of Phytogeography and Taxonomy 56 51 - 52 2008 [Refereed][Not invited]
  • Koh Nakamura, Tetsuo Denda, Osamu Kameshima, Masatsugu Yokota
    JOURNAL OF PLANT RESEARCH 120 (4) 501 - 509 0918-9440 2007/07 [Refereed][Not invited]
    We examined the floral morph of tetraploid Ophiorrhiza japonica Blume var. amamiana Hatus. and diploid O. japonica var. japonica to elucidate the association of distyly and ploidy levels. Chloroplast DNA phylogeny was reconstructed to determine the number of tetraploidization events and floral morph shifts in O. japonica. All individuals of O. japonica var. amamiana proved to be long-homostylous, whereas O. japonica var. japonica was distylous with typical long- and short-styled flowers. Distyly is related to the ploidy level. The bagging treatment of flowers indicated that O. japonica var. amamiana is self-compatible and potentially automatically self-pollinating. In cpDNA sequencing analysis, no haplotype was shared between the two varieties. The cpDNA haplotype network displayed the monophyly of O. japonica var. amamiana, suggesting a single origin of this variety. Hence, both tetraploidization and the breakdown of distyly to homostyly in O. japonica var. amamiana likely occurred just once. Because O. japonica var. amamiana having the morphological and cytological entity is recognized as a single lineage and clearly separated from O. japonica var. japonica, this variety can be considered to be a distinct species. We therefore propose to raise O. japonica var. amamiana to the rank of species.
  • Koh Nakamura, Shih-Wen Chung, Goro Kokubugata, Tetsuo Denda, Masatsugu Yokota
    JOURNAL OF PLANT RESEARCH 119 (6) 657 - 661 0918-9440 2006/11 [Refereed][Not invited]
    Hayataella (Rubiaceae) is a monotypic genus endemic to Taiwan that comprises H. michelloides. In recent years, Hayataella was considered to be synonymous with Ophiorrhiza; however, no specific data have been reported, and the systematic treatment of Hayataella has been unclear. To elucidate the systematic treatment of Hayataella, molecular phylogenetic analyses based on ITS of nrDNA, atp B-rbcL, and trnK/matK of cpDNA were conducted with four Ophiorrhiza species. In the Bayesian and the most parsimonious trees, H. michelloides was included in the Ophiorrhiza clade. The monotypic status of Hayataella is, therefore, not considered appropriate, and the combination Ophiorrhiza michelloides (Masam.) H. S. Lo is supported.
  • Karyotype of Ophiopogon reversus (Convallariaceae) from Taiwan and the Southern Ryukyus
    Tetsuo Denda, Koh Nakamura, Masatsugu Yokota
    Taiwania 51 117 - 122 2006 [Refereed][Not invited]
  • Homostyly and autogamy in Ophiorrhiza pumila (Rubiaceae) in the Ryukyu Archipelago
    Koh Nakamura, Tetsuo Denda, Masatsugu Yokota
    Journal of Japanese Botany 81 113 - 120 2006 [Refereed][Not invited]
  • 琉球列島産ソテツCycas revoluta Thunb.の種子形態について
    中村剛, 傳田哲郎, 横田昌嗣
    沖縄生物学会誌 (43) 53­57  2005 [Not refereed][Not invited]
  • Seed morphology of Cycas revoluta Thunberg (Cycadaceae) in the Ryukyu Archipelago
    Koh Nakamura, Tetsuo Denda, Masatsugu Yokota
    Biological Magazine Okinawa 43 53 - 57 2005 [Refereed][Not invited]
  • Choromosome numbers of Ophiorrhiza and Psychotria (Rubiaceae) in the Ryukyus
    Koh Nakamura, Tetsuo Denda, Osamu Kameshima, Mariko Uehara, Masatsugu Yokota
    Biological Magazine Okinawa 41 15 - 24 2003 [Refereed][Not invited]

Books etc

  • 通往世界的植物: 臺灣高山植物的時空旅史
    游旨价著, 中村剛, 李建成, 李攀, 趙建棣, 鍾國芳審訂 (Contributor臺灣,琉球群島與日本列島間的聯繋)
    春山出版 2020/03
  • Botanical illustrations by Chusuke Suzaki: plants from Mt. Taisetsu and other areas
    Masaru Katoo, Hideki Takahashi, Koh Nakamura, Sho Hayakawa 
    Hokkaido University Press 2016/06

Awards & Honors

  • 2013/05 Biological Society of Okinawa IKEHARA SADAO Prize
     Plant biogeography in the Ryukyus, Taiwan, and the Philippines 
    受賞者: Koh Nakamura
  • 2012/03 Japanese Society for Plant Systematics Young Scientist Award
     Plant biogeography in the Ryukyu Archipelago and Taiwan 
    受賞者: Koh Nakamura
  • 2007/03 Japanese Society for Plant Systematics Distinguished Oral Presentation Award
     Breakdown of distyly in a tetraploid variety of Ophiorrhiza japonica (Rubiaceae) and its phylogenetic analysis 
    受賞者: Koh Nakamura

Research Grants & Projects

  • 北海道等のカラフトグワイの遺伝的多様性を守る生息域外保全事業
    Date (from‐to) : 2019 -2021 
    Author : 中村剛
  • 極東ロシアとの比較による,北海道指定希少植物の固有性,集団分化の検証と保全提言
    Date (from‐to) : 2016/04 -2020/03 
    Author : 中村剛
  • 北海道崕山固有キリギシソウの遺伝的多型を守る生息域外保全事業
    Date (from‐to) : 2018 -2020 
    Author : 中村剛
  • 国境を越えて分布する北海道指定希少野生植物をモデルとした,国際共同保全システムの確立
    Date (from‐to) : 2016/04 -2019/03 
    Author : 中村剛
  • ユウバリクモマグサの生息域外保全のための生育地調査及び種子等採集活動
    Date (from‐to) : 2019 -2019 
    Author : 中村剛
  • オニオトコヨモギの生息域外保全のための生育地調査及び種子等採集活動
    Date (from‐to) : 2018 -2018 
    Author : 中村剛
  • 北海道の自然を特徴づける湿地植物の保全遺伝学的研究
    Date (from‐to) : 2015/04 -2016/03 
    Author : 中村剛
  • 博士研究員研究奨励費
    Date (from‐to) : 2014/01 -2015/03 
    Author : 中村剛
  • 招聘博士研究員研究奨励費
    台湾中央研究院 生命科学組:
    Date (from‐to) : 2012/01 -2013/12 
    Author : 中村剛
  • 招聘博士研究員研究奨励費
    台湾中央研究院 生命科学組:
    Date (from‐to) : 2010/02 -2011/12 
    Author : 中村剛
  • 琉球列島とフィリピン,オーストラリアに隔離分布する植物の系統地理学的解析
    Date (from‐to) : 2008/04 -2009/03 
    Author : 中村剛
  • 琉球列島産植物の系統地理パタンにおける,地史的,生態学的要因に関する研究
    Date (from‐to) : 2007/04 -2008/03 
    Author : 中村剛
  • 琉球列島産陸上維管束植物の系統地理学的研究
    Date (from‐to) : 2004/04 -2007/03 
    Author : 中村剛

Educational Activities

Teaching Experience

  • Inter-Graduate School Classes(General Subject):Natural and Applied Sciences
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 生態学、北方生態系、北海道、植物、動物、昆虫、魚類、森林、山岳、ツンドラ、沿岸、河川、湿原、相互作用、外来種、野生作物、気候変動 ecology, northern ecosystem, Hokkaido, plants, animals, insects, fishes, forest, mountain, tundra, seacoast, river, wetland, interaction, invasive species, field crop, climate change
  • Fundamental Course in Biodiversity of Northern Ecosystems
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 環境科学院
    キーワード : 生態学、北方生態系、北海道、植物、動物、昆虫、魚類、森林、山岳、ツンドラ、沿岸、河川、湿原、相互作用、外来種、野生作物、気候変動 ecology, northern ecosystem, Hokkaido, plants, animals, insects, fishes, forest, mountain, tundra, seacoast, river, wetland, interaction, invasive species, field crop, climate change
  • Advanced Course in Agro-Ecosystem Science I (Crop Production)
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 環境科学院
    キーワード : 作物生産 寒冷積雪地 遺伝資源 資源の探索・改良 作型 農耕地の環境保全 植物系統地理学 保全生態学 Crop production, Cool and snow cover region, Exploitation and estimation of plant resource, Improvement of crop characteristics, cropping system, Environmental condition of agricultural field, Plant phylogeography, Conservation biology
  • Advanced Ecology and Systematics I
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 農学院
    キーワード : 系統学、進化、最節約原理、系統樹、最尤法、距離法、ネットワーク、分類群、博物館、標本、多様性データベース
  • Inter-Graduate School Classes(General Subject):Natural and Applied Sciences
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 系統学、進化、最節約原理、系統樹、最尤法、距離法、ネットワーク、分類群、博物館、標本、多様性データベース
  • Agricultural Practice
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 農学部
    キーワード : 農場 農業体験 作物生産 家畜飼養 収穫
  • Systematic Botany
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 農学部
    キーワード : 植物分類体系,系統,植物地理,絶滅危惧植物,植物園,植生,植生復元,保護・保全,標本

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