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Material collection for comprehensive phylogeny of the family Dipterocarpaceae

Research Project

Project/Area Number 17405032
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section海外学術
Research Field 林学・森林工学
Research InstitutionKyushu University

Principal Investigator

ALFRED E  Kyushu University, Szmidt Department of Biology, Associate Professor (70325497)

Co-Investigator(Kenkyū-buntansha) INOMATA Nobuyuki  Kyushu University, Inomata of Biology, Assistant Professor (20301335)
Project Period (FY) 2005 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥14,330,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥930,000)
Fiscal Year 2007: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2006: ¥4,700,000 (Direct Cost: ¥4,700,000)
Fiscal Year 2005: ¥5,600,000 (Direct Cost: ¥5,600,000)
Keywordspopulation genetics / evolution / internet database / population genetics / evolution / internet database / 集団遺伝学
Research Abstract

1. One month long trip was made to India and Sri Lanka. During the trip samples were collected from 15 species from Dipterocarpaceae family occurring in the Indian Western Ghats and Sri Lanka. Together with samples collected previously, we now possess samples representing all genera of this family occurring in Asia. In addition, samples were collected in populations of the following mangrove species: Bruguiera gymnorrhiza, B. sexangula and Rhizophora apiculata.
2. First comprehensive molecular phylogeny of the sub-family Dipterocarpoideae based on chloroplast DNA sequences was published (Gamage, et. al. 2006).
3. One MSc thesis was completed (Aoi Saitoh).
4. Material from populations of four species from the genus Shorea occurring in Indonesia.
5. Samples obtained from Indonesia have been used for a study of geographic history of Shorea parvifolia . It is based on analysis of DNA polymorphism in two nuclear gene loci.
6. MySQL powered database containing list of all samples stored in our la … More boratory(including those procured in the present project) is available for public access on the following website: http://genetics.biology.kyushu-u.ac.jp.
7. Ten days trip was made to Thailand. During this trip we collected samples from more than 30 additional species of Dipterocarpaceae from different parts of the country. In addition, we also collected samples from two mangrove species: Rhizophora apiculata and R. mucronata. Furthermore, samples of additional species of Dipterocarpaceae were also collected in southern China.
8. Seven papers have been published in the following international journals: Heredity, Molecular Biology and Evolution, Genes and Genetic Systems, Canadian Journal of Forest Research and Tree Genetics and Genomes.
9. One BSc (Iwaya Chihiro) and three PhD theses (Ishiyama Hiroko, Ismael Khatab, Araki T. Neyton)were defended at the Department of Biology, Kyushu University.
10. Seven presentations were made at international conferences in Japan, Spain, Germany and United Kingdom.
11. The operating system of our web server hosting the sample database has been replaced with the latest version of SuSE Linux 10.3. An upgrade has also been to MySQL server, which powers our database and to the Apache web service. Disk space has been extended by 500 GB.
12. A new literature database containing more than 160000 references has been built and is currently being prepared for public deployment on our server Less

Report

(4 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (37 results)

All 2008 2007 2006 2005

All Journal Article (22 results) (of which Peer Reviewed: 10 results) Presentation (15 results)

  • [Journal Article] Phylogeography of Larix sukaczewii Dyl. and L. sibirica L. inferred from nucleotide variation of nuclear genes2008

    • Author(s)
      Araki, N.H.T., Khatab, I.A., Hemamali, K. K.G U., Inomata, N., Wang, X-R.and Szmidt, A.E
    • Journal Title

      Tree Genetics and Genomes (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Demographic history and interspecific hybridization of four Shorea species (Diptero carpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions2008

    • Author(s)
      Ishiyama, H., Inomata, N., Yamazaki, T., Ab Shukor, N. A.and Szmidt, A.E
    • Journal Title

      Canadian Journal of Forest Research (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes2008

    • Author(s)
      Khatab, I.A., Ishiyama, H., Inomata N., Wang, X-R.and Szmidt, A.E
    • Journal Title

      Genes and Genetic Systems 83

      Pages: 55-66

    • NAID

      10024395507

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Phylogeography of Larix sukaczewii Dyl. and L. sibirica L. inferred from nucleotide variation of nuclear genes2008

    • Author(s)
      N. H. T., Araki, I. A., Khatab, K. K. G. U., Hemamali, N., Inomata, X-R., Wang, A. E.,Szmidt
    • Journal Title

      Tree Genetics and Genomes (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions2008

    • Author(s)
      H., Ishiyama, N., Inomata, T., Yamazaki, N. A., Ab Shukor, A. E., Szmidt
    • Journal Title

      Canadian Journal of Forest Research (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes2008

    • Author(s)
      I. A., Khatab, H., Ishiyama, N., Inomata, X-R., Wang, A. E., Szmidt
    • Journal Title

      Genes and Genetic Systems 83(1)

      Pages: 55-66

    • NAID

      10024395507

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Phylogeography of Larix sukaczewii Dyl. and L.sibirica L. inferred from nucleotide variation of nuclear genes2008

    • Author(s)
      Araki, N.H.T., Khatab, I.A., Hemamali, K.K.G.U., Inomata, N., Wang, X-R. and Szmidt, A.E.
    • Journal Title

      Tree Genetics and Gennomes (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Demographic history and interspecific hybridization of four Shorea species(Dipterocarpaceae)from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions2008

    • Author(s)
      Ishiyama, H., Inomata, N., Yamazaki, T., Ab Shukor, N.A. and Szmidt, A.E.
    • Journal Title

      Canadian Journal of Forest Research (In press)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes2008

    • Author(s)
      Khatab, I.A., Ishiyama, H., Inomata, Wang, N., X-R. and Szmidt, A.E.
    • Journal Title

      Genes and Genetic Systems 83(1)

      Pages: 55-66

    • NAID

      10024395507

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci2006

    • Author(s)
      Ma, X-F., Szmidt, A.E.and Wang, X-R
    • Journal Title

      Molecular Biology and Evolution 23

      Pages: 807-816

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Diptero carpaceae) based on chloroplast DNA sequences2006

    • Author(s)
      Gamage, D.T., de Silva, M.P., Inomata, N., Yamazaki, T.and Szmidt, A.E
    • Journal Title

      Genes and Genetic Systems 81

      Pages: 1-12

    • NAID

      10017408045

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci2006

    • Author(s)
      X-F., Ma, A. E., Szmidt, X-R., Wang
    • Journal Title

      Molecular Biology and Evolution 23

      Pages: 807-816

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences.2006

    • Author(s)
      D. T., Gamage, M. P., de Silva, N., Inomata, T., Yamazaki, A. E., Szmidt
    • Journal Title

      Genes and Genetic Systems 81

      Pages: 1-12

    • NAID

      10017408045

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci2006

    • Author(s)
      Ma, X-F., Szmidt, A.E., Wang, X-R.
    • Journal Title

      Molecular Biology and Evolution 23

      Pages: 807-816

    • Related Report
      2006 Annual Research Report 2005 Annual Research Report
  • [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences2006

    • Author(s)
      Gamage, D.T., de Silva, M.P., Inomata, N., Yamazaki, T., Szmidt, A.E.
    • Journal Title

      Genes and Genetic Systems 81

      Pages: 1-12

    • NAID

      10017408045

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences2006

    • Author(s)
      Gamage, D.T., de Silva, M.P., Inomata, N., Yamazaki, T., Szmidt, A.E.
    • Journal Title

      Genes and Genetic Systems (In press)

    • NAID

      10017408045

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster2005

    • Author(s)
      Goto, I-I., Szmidt, A.E., Yamazaki, T.and Inomata, N
    • Journal Title

      Heredity 95

      Pages: 369-376

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Few loose observations from the Swedish and Japanese universities2005

    • Author(s)
      Szmidt, A.E
    • Journal Title

      Comparative Physiology and Biochemistry 21

      Pages: 175-176

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster2005

    • Author(s)
      H., Goto, A. E., Szmidt, T., Yamazaki, N., Inomata
    • Journal Title

      Heredity 95

      Pages: 369-376

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Few loose observations from the Swedish and Japanese universities2005

    • Author(s)
      A. E., Szmidt
    • Journal Title

      Comparative Physiology and Biochemistry 21

      Pages: 175-176

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster2005

    • Author(s)
      Goto, H., Szmidt, A.E., Yamazaki, T., Inomata, N.
    • Journal Title

      Heredity 95

      Pages: 369-376

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Few loose observations from the Swedish and Japanese universities2005

    • Author(s)
      Szmidt, A.E.
    • Journal Title

      Comparative Physiology and Biochemistry 21

      Pages: 175-176

    • Related Report
      2005 Annual Research Report
  • [Presentation] Demographic history of Larix sibirica and L. sukaczewii inferred from nucleotide variation of nuclear genes2007

    • Author(s)
      Khatab, I., Ishiyama, H., Inomata, N.and Szmidt, A.E
    • Organizer
      79-th Meeting of the Genetic Society of Japan
    • Place of Presentation
      Okayama,Japan
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes2007

    • Author(s)
      Khatab, I., Ishiyama, H., Inomata, N.and Szmidt, A.E
    • Organizer
      41-st Annual Meeting of the Population Genetics Group, University of Warwick
    • Place of Presentation
      Warwick,UK
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Demographic history of Larix sibirica and L. sukaczewii inferred from nucleotide variation of nuclear genes2007

    • Author(s)
      I., Khatab, H., Ishiyama, N., Inomata, A. E., Szmidt
    • Organizer
      79-th Meeting of the Genetic Society of Japan
    • Place of Presentation
      Okayama Japan
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes2007

    • Author(s)
      I., Khatab, H., Ishiyama, N., Inomata A. E., Szmidt
    • Organizer
      41-st Annual Meeting of the Population Genetics Group, University of Warwick, UK
    • Place of Presentation
      Warwick, UK
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Demographic histoly of Larix sibirica and L.sukaczewii inferred from nucleotide variation of nuclear genes2007

    • Author(s)
      Khatab, I., Ishiyama, H., Inomata, N. and Szmidt, A.E.
    • Organizer
      79-th Meeting of the Genetic Society of Japan
    • Place of Presentation
      岡山
    • Related Report
      2007 Annual Research Report
  • [Presentation] The demographic history of Shorea parvifolia (Dipterocarpaceae) inferred from nucleotide polymorphism at multiple nuclear genes2006

    • Author(s)
      Ishiyama, H., Khatab, I., Finkeldey, R., Inomata, N., Tsumura, H., Yamazaki, T.and Szmidt, A.E
    • Organizer
      Population Genetics and Genomics of Forest Trees: From Gene Function to Evolutionary Dynamics and Conservation, IUFRO
    • Place of Presentation
      Madrid,Spain
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Patterns of nucleotide polymorphism in the 4CL nuclear gene region of Eurasian Laiix species2006

    • Author(s)
      Khatab, I., Ishiyama, H., Saitoh, A., Inomata, N., and Szmidt, A. E
    • Organizer
      Population Genetics and Genomics of Forest Trees: From Gene Function to Evolutionary Dynamics and Conservation, IUFRO
    • Place of Presentation
      Madrid,Spain
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Pattern of nucleotide polymorphism in the gMdh nuclear gene region of Eurasian Larix (Pinaceae) species2006

    • Author(s)
      Saitoh, A., Araki, N.H.T., Inomata, N.and Szmidt A.E
    • Organizer
      Population Genetics and Genomics of Forest Trees: From Gene Function to Evolutionary Dynamics and Conservation, IUFRO
    • Place of Presentation
      Madrid,Spain
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The evolutionary forces affecting nucleotide polymorphism in natural populations of Shorea parvifoha (Dipterocarpaceae)2006

    • Author(s)
      Ishiyama, H., Khatab, I.Finkeldey, R., Inomata, N., Yamazaki, T. and Szmidt A.E
    • Organizer
      19th Annual Conference of the section Plant population Biology of the Ecological Society of Germany, Switzerland and Austria
    • Place of Presentation
      Halle,Germany
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Phylogeography of larches (Larix spp Mill.) from Russia based on DNA variation of a nuclear gene2006

    • Author(s)
      Khatab, I., Ishiyama, H., Inomata, N.and Szmidt, A.E
    • Organizer
      19th Annual Conference of the section Plant population Biology of the Ecological Society of Germany, Switzerland and Austria
    • Place of Presentation
      Halle,Germany
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The demographic history of Shorea parvifolia(Dipterocarpaceae) inferred from nucleotide polymorphism at multiple nuclear genes2006

    • Author(s)
      H., Ishiyama, I., Khatab, R., Finkeldey, N., Inomata, H., Tsumura, T., Yamazaki, A. E., Szmidt
    • Organizer
      Population Genetics and Genomics of Forest Trees : From Gene Function to Evolutionary Dynamics and Conservation, IUFRO
    • Place of Presentation
      Madrid, Spain
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Patterns of nucleotide polymorphism in the 4CL nuclear gene region of Eurasian Larix species2006

    • Author(s)
      I., Khatab, H., Ishiyama, A., Saitoh, N., Inomata, A. E., Szmidt
    • Organizer
      Population Genetics and Genomics of Forest Trees : From Gene Function to Evolutionary Dynamics and Conservation, IUFRO
    • Place of Presentation
      Madrid Spain
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Pattern of nucleotide polymorphism in the gMdh nuclear gene region of Eurasian Larix(Pinaceae) species2006

    • Author(s)
      A., Saitoh, N. H. T., Araki, N., Inomata, A. E., Szmidt
    • Organizer
      Population Genetics and Genomics of Forest Trees : From Gene Function to Evolutionary Dynamics and Conservation, IUFRO
    • Place of Presentation
      Madrid Spain
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] The evolutionary forces affecting nucleotide polymorphism in natural populations of Shorea parvifolia(Dipterocarpaceae)2006

    • Author(s)
      H., Ishiyama, I., Khatab, R., Finkeldey, N., Inomata, T., Yamazaki, A. E., Szmidt
    • Organizer
      The evolutionary forces affecting nucleotide polymorphism in natural populations of Shorea parvifolia(Dipterocarpaceae).
    • Place of Presentation
      Halle, Germany
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Phylogeography of larches(Larix spp Mill.) from Russia based on DNA variation of a nuclear gene2006

    • Author(s)
      I., Khatab, H., Ishiyama, N., Inomata, A. E., Szmidt
    • Organizer
      19th Annual Conference of the section Plant Population Biology of the Ecological and Austria
    • Place of Presentation
      Halle, Germany
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary

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Published: 2005-04-01   Modified: 2016-04-21  

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