研究者業績

Naoyuki Nakahama

  (中濱 直之)

Profile Information

Affiliation
University of Hyogo, University of Hyogo
主任研究員, 自然・環境再生研究部, 兵庫県立人と自然の博物館
Degree
博士 (農学)(京都大学)

Researcher number
50807592
J-GLOBAL ID
201701017634263730
researchmap Member ID
B000273321

External link

野外調査及び遺伝解析による保全生態学が主な研究分野ですが、それに限らず群集生態学、保全遺伝学、生物間相互作用、送粉生態学、生物多様性科学、Museomics、標本保存科学、分子系統学など多岐にわたった研究活動を展開しております。共同研究のお誘いや普及啓発活動のご依頼、進路のご相談などお気軽にご相談ください。(こちらに連絡先を記載しております。)


Major Papers

 70
  • Naoyuki Nakahama, Tomohiro Furuta, Haruko ANdo, Suzuki Setsuko, Atsushi Takayanagi, Yuji ISagi
    Forest Ecology and Management, 484 118637-118637, Mar, 2021  Peer-reviewedLead authorCorresponding author
  • Naoyuki Nakahama
    Ecological Research, 36(1) 13-23, Jan, 2021  Peer-reviewedInvited
  • Naoyuki Nakahama, Kei Uchida, Asuka Koyama, Takaya Iwasaki, Masaaki Ozeki, Takeshi Suka
    Biodiversity and Conservation, 29(7) 2201-2215, 2020  Peer-reviewedLead authorCorresponding author
  • Jeff Ollerton, Sigrid Liede-Schumann, Mary E Endress, Ulrich Meve, André Rodrigo Rech, Adam Shuttleworth, Héctor A Keller, Mark Fishbein, Leonardo O Alvarado-Cárdenas, Felipe W Amorim, Peter Bernhardt, Ferhat Celep, Yolanda Chirango, Fidel Chiriboga-Arroyo, Laure Civeyrel, Andrea Cocucci, Louise Cranmer, Inara Carolina da Silva-Batista, Linde de Jager, Mariana Scaramussa Deprá, Arthur Domingos-Melo, Courtney Dvorsky, Kayna Agostini, Leandro Freitas, Maria Cristina Gaglianone, Leo Galetto, Mike Gilbert, Ixchel González-Ramírez, Pablo Gorostiague, David Goyder, Leandro Hachuy-Filho, Annemarie Heiduk, Aaron Howard, Gretchen Ionta, Sofia C Islas-Hernández, Steven D Johnson, Lize Joubert, Christopher N Kaiser-Bunbury, Susan Kephart, Aroonrat Kidyoo, Suzanne Koptur, Cristiana Koschnitzke, Ellen Lamborn, Tatyana Livshultz, Isabel Cristina Machado, Salvador Marino, Lumi Mema, Ko Mochizuki, Leonor Patrícia Cerdeira Morellato, Chediel K Mrisha, Evalyne W Muiruri, Naoyuki Nakahama, Viviany Teixeira Nascimento, Clive Nuttman, Paulo Eugenio Oliveira, Craig I Peter, Sachin Punekar, Nicole Rafferty, Alessandro Rapini, Zong-Xin Ren, Claudia I Rodríguez-Flores, Liliana Rosero, Shoko Sakai, Marlies Sazima, Sandy-Lynn Steenhuisen, Ching-Wen Tan, Carolina Torres, Kristian Trøjelsgaard, Atushi Ushimaru, Milene Faria Vieira, Ana Pía Wiemer, Tadashi Yamashiro, Tarcila Nadia, Joel Queiroz, Zelma Quirino
    Annals of Botany, 123(2) 311-325, Jan 23, 2019  Peer-reviewed
    Background and Aims Large clades of angiosperms are often characterized by diverse interactions with pollinators, but how these pollination systems are structured phylogenetically and biogeographically is still uncertain for most families. Apocynaceae is a clade of >5300 species with a worldwide distribution. A database representing >10 % of species in the family was used to explore the diversity of pollinators and evolutionary shifts in pollination systems across major clades and regions.Methods The database was compiled from published and unpublished reports. Plants were categorized into broad pollination systems and then subdivided to include bimodal systems. These were mapped against the five major divisions of the family, and against the smaller clades. Finally, pollination systems were mapped onto a phylogenetic reconstruction that included those species for which sequence data are available, and transition rates between pollination systems were calculated.Key Results Most Apocynaceae are insect pollinated with few records of bird pollination. Almost three-quarters of species are pollinated by a single higher taxon (e.g. flies or moths); 7 % have bimodal pollination systems, whilst the remaining approx. 20 % are insect generalists. The less phenotypically specialized flowers of the Rauvolfioids are pollinated by a more restricted set of pollinators than are more complex flowers within the Apocynoids + Periplocoideae + Secamonoideae + Asclepiadoideae (APSA) clade. Certain combinations of bimodal pollination systems are more common than others. Some pollination systems are missing from particular regions, whilst others are over-represented.Conclusions Within Apocynaceae, interactions with pollinators are highly structured both phylogenetically and biogeographically. Variation in transition rates between pollination systems suggest constraints on their evolution, whereas regional differences point to environmental effects such as filtering of certain pollinators from habitats. This is the most extensive analysis of its type so far attempted and gives important insights into the diversity and evolution of pollination systems in large clades.
  • Naoyuki Nakahama, Yuji Isagi, Moron Ito
    EUROPEAN JOURNAL OF ENTOMOLOGY, 116 486-491, 2019  Peer-reviewedLead authorCorresponding author
    Dried specimens of insects are increasingly seen as genetic resources. However, genetic analysis of dried specimens of insects is hampered by the deterioration of the DNA. In this study, we developed methods for preparing dried specimens of insects with well-preserved DNA, mainly for PCR-based genetic analysis. First, we compared the effects of either exposure to ethyl acetate vapour for from 10 min to 6 h or by freezing on the fragmentation of DNA in order to determine optimal length of time needed for killing insects using the above methods. Second, we compared the fragmentation of DNA after preservation by drying or immersion of legs in 99.5% ethanol or 99% propylene glycol in 0.2-ml tubes. We assessed degrees of fragmentation of DNA by determining polymerase chain reaction (PCR) success rates with primers for 313-, 710- and 1555-bp fragments using DNA that was collected immediately, and at one, six and 12 months after preparing the specimens. Differing times taken to kill insects did not affect the fragmentation of DNA. In dried specimens, DNA was seriously fragmented after one month, whereas that in legs prepared by immersion in 99.5% ethanol or 99% propylene glycol contained long fragments of DNA (1555 bp-) after 12 months. Propylene glycol was more suitable for preservation than ethanol, because the latter evaporates. Thus, to preserve insect DNA we suggest inserting the pin on which an insect is impaled into the hinged lid of a 0.2-ml tube containing 99% propylene glycol so that when the lid is closed the legs of the insect are preserved in the solution.
  • Naoyuki Nakahama, Kei Uchida, Atushi Ushimaru, Yuji Isagi
    Heredity, 121(2) 155-168, Aug, 2018  Peer-reviewedLead authorCorresponding author
    Semi-natural grassland areas expanded worldwide several thousand years ago following an increase in anthropogenic activities. However, semi-natural grassland habitat areas have been declining in recent decades due to changes in landuse, which have caused a loss of grassland biodiversity. Reconstructing historical and recent demographic changes in semi-natural grassland species will help clarify the factors affecting their population decline. Here we quantified past and recent demographic histories of Melitaea ambigua (Lepidoptera; Nymphalidae), an endangered grassland butterfly species in Japan. We examined changes in demography over the past 10,000 years based on 1378 bp of mitochondrial COI gene. We then examined changes in its genetic diversity and structure during the last 30 years using nine microsatellite DNA markers. The effective population size of M. ambigua increased about 3000-6000 years ago. In contrast, the genetic diversity and effective population sizes of many populations significantly declined from the 1980s to 2010s, which is consistent with a recent decline in the species population size. Our data suggest that the M. ambigua demography can be traced to changes in area covered by semi-natural grasslands throughout the Holocene.
  • Naoyuki Nakahama, Yuji Isagi
    INSECT CONSERVATION AND DIVERSITY, 11(4) 330-340, Jul, 2018  Peer-reviewedLead authorCorresponding author
    The monitoring of genetic characters and definition of effective conservation units are important for conservation of endangered semi-natural grassland species.Using molecular markers, we elucidated the recent transitions in genetic diversity for the endangered grassland butterfly Melitaea protomedia (Lepidoptera; Nymphalidae) in Japan. First, we examined changes in genetic diversity and structure from the 1980s to the 2010s from archival and contemporary DNA samples using eight microsatellite markers. Second, we estimated the genetic structure based on 1374bp of mitochondrial COI gene from contemporary samples. We also defined the conservation units of M. protomedia based on the above analysis.The genetic diversity of M. protomedia has significantly declined from the 1980s to the 2010s. Although genetic differentiation was very strong among populations in c. 2010, there was only weak genetic structure in c. 1990. In addition, the number of haplotypes based on mitochondrial DNA is now very low due to recent declines.These findings suggest that effective conservation units for critically endangered species should be determined based on historic (i.e. prior to population declines) as well as contemporary genetic diversity and differentiation, because genetic structure may have changed over time. Genetic analysis of archival DNA is useful to obtain historic genetic information.
  • Naoyuki Nakahama, Michimasa Yamasaki, Atsushi Takayanagi
    ENTOMOLOGICAL SCIENCE, 19(3) 268-274, Jul, 2016  Peer-reviewedLead authorCorresponding author
    In recent years, the increase in sika deer populations has had a significant impact on forest ecosystems. Many studies have reported that this increase has led to the dominance of plants unpalatable to the deer; however, few studies have investigated the effects of this dominance on the specialist sawfly species that feed on the unpalatable plants. We observed the mass emergence of Aglaostigma amoorensis (Hymenoptera: Tenthredinidae), a rare specialist sawfly of the false helleborine Veratrum plants unpalatable to sika deer, in areas under severe feeding pressure by sika deer. An exponential increase in the number of emergent A.amoorensis adults was observed to occur with an increase in Veratrum album patch sizes. In addition, the increase in the A.amoorensis density had a negative effect on reproductive success of V.album. Our findings suggest that the relative abundance of specialist sawfly to the host-plant abundance has changed for successive years after sika deer irruption.
  • Naoyuki Nakahama, Kei Uchida, Atushi Ushimaru, Yuji Isagi
    AGRICULTURE ECOSYSTEMS & ENVIRONMENT, 221 20-27, Apr, 2016  Peer-reviewedLead authorCorresponding author
    Recent global land-use changes have led to reductions in many herbaceous plant species in semi-natural grassland landscapes. Changes in management frequency and intensity are known to cause declines in plant populations. However, little is known about the impact of changes in the timing of management practices on the genetic diversity as well as the reproductive success of rare semi-natural grassland species. We determined the suitable management (mowing) timing for Vincetoxicum pycnostelma Kitag. (Apocynaceae; Asclepiadoideae), an endangered summer- and autumn-blooming semi-natural grassland herb. We examined 15 V. pycnostelma populations to assess the effects of mowing timing on the genetic diversity of each population using nine microsatellite markers and on pollination and reproductive success. Pollination success was not affected by flowering timing. Mowing during the mid- to late flowering and fruiting periods of V. pycnostelma (July-September) had a significant negative effect on the number of inflorescences and total fruits produced, whereas mowing before flowering and growing periods (April, May and November-March) had positive effects on the number of inflorescences and fruits, respectively. Furthermore, mowing during the mid- to late flowering and fruiting periods also caused a significant decrease in genetic diversity. Our results demonstrated that mowing events during the mid- to late flowering and fruiting periods caused significant declines in the genetic diversity and/or reproductive success of V pycnostelma. By contrast, mowing before flowering periods significantly enhanced reproductive success. To conserve semi-natural grassland herb diversity, mowing should be avoided during seasons when the flowering and fruiting periods of many endangered species overlap. (C) 2016 Elsevier B.V. All rights reserved.
  • Naoyuki Nakahama, Yuki Hirasawa, Tsubasa Minato, Masahiro Hasegawa, Yuji Isagi, Takashi Shiga
    PLANT ECOLOGY, 216(12) 1635-1647, Dec, 2015  Peer-reviewedLead authorCorresponding author
    The reintroduction of ex situ conserved individuals is an important approach for conserving threatened plants and reducing extinction risk. In this study, we elucidated the effects on the genetic diversity of wild populations of Vincetoxicum pycnostelma Kitag. [=Cynanchum paniculatum (Bunge) Kitag.] by modelling the genetic consequences of reintroducing plants using the germinated seeds of herbarium specimens. This semi-natural grassland herb is threatened in Japan. First, we tested the germinability of seeds from herbarium specimens collected from nine sites in Kinki and Tokai districts, Japan (one specimen per site, total 206 seeds). Next, we analysed the genetic diversity and structure of germinated seedlings and the current wild individuals using nine polymorphic microsatellite markers. Germination was observed for 38 seeds (18.4 %) from four specimens collected 3-18 years prior to the study. Although the genetic diversity of the specimens' seeds was lower than that of the wild population because of the small sample size, the seedlings from specimens taken from three sites had unique alleles that did not exist in the wild populations. Consequently, viable herbarium specimens' seeds with unique alleles could be useful resources for recovering the genetic diversity in threatened wild plant populations.

Misc.

 12

Books and Other Publications

 3
  • 中濱直之 (Role: Contributor, 生物標本の遺伝情報を利用する(PP.232-237))
    神戸新聞総合出版センター, Mar, 2023 (ISBN: 9784343011893)
  • 岡山県野生動植物調査検討会 (Role: Contributor, ガロアムシの一種)
    岡山県環境文化部自然環境課, Mar, 2020
  • 加納康嗣, 冨永修, 市川顕彦, 伊藤ふくお, 内舩俊樹, 中濵直之, 西川勝, 中峰空, 旭和也, 遠藤拓也, 小松謙之, 河合正人, 村井貴史 (Role: Contributor, ガロアムシ目)
    (株)学研プラス, May, 2016

Presentations

 81

Teaching Experience

 7

Major Research Projects

 19

Social Activities

 48