Material collection for comprehensive phylogeny of the family Dipterocarpaceae

• Project/Area Number: 17405032
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 海外学術
• Research Field: 林学・森林工学
• Research Institution: Kyushu 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: ¥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)
• Keywords: population 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 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

Research Products

• [Journal Article] Phylogeography of Larix sukaczewii Dyl. and L. sibirica L. inferred from nucleotide variation of nuclear genes (2008)
  • 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
  • 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 regions (2008)
  • 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
  • Peer Reviewed
• [Journal Article] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes (2008)
  • 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
  • Peer Reviewed
• [Journal Article] Phylogeography of Larix sukaczewii Dyl. and L. sibirica L. inferred from nucleotide variation of nuclear genes (2008)
  • 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
• [Journal Article] Demographic history and interspecific hybridization of four Shorea species (Dipterocarpaceae) from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions (2008)
  • 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
• [Journal Article] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes (2008)
  • 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
• [Journal Article] Phylogeography of Larix sukaczewii Dyl. and L.sibirica L. inferred from nucleotide variation of nuclear genes (2008)
  • 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)
  • Peer Reviewed
• [Journal Article] Demographic history and interspecific hybridization of four Shorea species(Dipterocarpaceae)from Peninsular Malaysia inferred from nucleotide polymorphism in nuclear gene regions (2008)
  • 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)
  • Peer Reviewed
• [Journal Article] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes (2008)
  • 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
  • Peer Reviewed
• [Journal Article] Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci (2006)
  • 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
  • Peer Reviewed
• [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Diptero carpaceae) based on chloroplast DNA sequences (2006)
  • 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
  • Peer Reviewed
• [Journal Article] Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci (2006)
  • 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
• [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
• [Journal Article] Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci (2006)
  • Author(s): Ma, X-F., Szmidt, A.E., Wang, X-R.
  • Journal Title: Molecular Biology and Evolution 23 Pages: 807-816
• [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences (2006)
  • 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
• [Journal Article] Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences (2006)
  • 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
• [Journal Article] Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster (2005)
  • 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
  • Peer Reviewed
• [Journal Article] Few loose observations from the Swedish and Japanese universities (2005)
  • 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
  • Peer Reviewed
• [Journal Article] Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster (2005)
  • 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
• [Journal Article] Few loose observations from the Swedish and Japanese universities (2005)
  • 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
• [Journal Article] Effect of nucleotide polymorphism in cis-regulatory and coding regions on amylase activity and fitness in Drosophila melanogaster (2005)
  • Author(s): Goto, H., Szmidt, A.E., Yamazaki, T., Inomata, N.
  • Journal Title: Heredity 95 Pages: 369-376
• [Journal Article] Few loose observations from the Swedish and Japanese universities (2005)
  • Author(s): Szmidt, A.E.
  • Journal Title: Comparative Physiology and Biochemistry 21 Pages: 175-176
• [Presentation] Demographic history of Larix sibirica and L. sukaczewii inferred from nucleotide variation of nuclear genes (2007)
  • 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
• [Presentation] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes (2007)
  • 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
• [Presentation] Demographic history of Larix sibirica and L. sukaczewii inferred from nucleotide variation of nuclear genes (2007)
  • 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
• [Presentation] Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes (2007)
  • 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
• [Presentation] Demographic histoly of Larix sibirica and L.sukaczewii inferred from nucleotide variation of nuclear genes (2007)
  • 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
• [Presentation] The demographic history of Shorea parvifolia (Dipterocarpaceae) inferred from nucleotide polymorphism at multiple nuclear genes (2006)
  • 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
• [Presentation] Patterns of nucleotide polymorphism in the 4CL nuclear gene region of Eurasian Laiix species (2006)
  • 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
• [Presentation] Pattern of nucleotide polymorphism in the gMdh nuclear gene region of Eurasian Larix (Pinaceae) species (2006)
  • 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
• [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
• [Presentation] Phylogeography of larches (Larix spp Mill.) from Russia based on DNA variation of a nuclear gene (2006)
  • 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
• [Presentation] The demographic history of Shorea parvifolia(Dipterocarpaceae) inferred from nucleotide polymorphism at multiple nuclear genes (2006)
  • 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
• [Presentation] Patterns of nucleotide polymorphism in the 4CL nuclear gene region of Eurasian Larix species (2006)
  • 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
• [Presentation] Pattern of nucleotide polymorphism in the gMdh nuclear gene region of Eurasian Larix(Pinaceae) species (2006)
  • 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
• [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
• [Presentation] Phylogeography of larches(Larix spp Mill.) from Russia based on DNA variation of a nuclear gene (2006)
  • 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