Grant-in-Aid for Scientific Research (Specially Designated Research Promotion)

Development and disclosure of the Yamashina Institute for Ornithology database system (2009 - )

The institute has been receiving science research grant from the Ministry of Education, Culture, Sports, Science and Technology and has conducted such research as "research on survival and recovery of rare birds" (2001-2004) and "research on organization and utilization of Japanese bird species materials" (2005-2008), and has been working on "development and disclosure of Yamashina Institute for Ornithology Database System" since 2009.

(From the newsletter Yamashina Choken News, September 1, 2009)

The Collections at the Yamashina Institute for Ornithology and the International Responsibility

The significant research asset of the Yamashina Institute for Ornithology that cannot be found in any other Japanese universities or research institutions includes avian specimens, library collection and bird banding data. The institute has already been conducting research focusing on these in the second phase of its research activities. The third phase intends to further develop the research focusing on the utilization of avian specimens and banding data.

As for biodiversity information, international projects such as GBIF(*1) and International Barcode of Life Project (DNA barcoding)(*2) have been launched in the recent years for facilitating information exchange. However, little information is being provided from Asian countries including Japan.

The avian specimens and banding data at the Yamashina Institute for Ornithology are one of the most abundant sources of biodiversity information in Asia, but need to be further organized (or digitalized) for it to be disseminated internationally.

This research aims to send out data to the existing international projects and to create and disseminate biodiversity information from a new perspective so that the Yamashina Institute for Ornithology can become Asia's center for bioinformatics and fulfill its international obligations.

Information Dissemination for International Projects

Three types of information have been identified for information dissemination to the existing international projects. These are bird banding data, archived specimens data and DNA sequence data.

As for bird banding data, we are currently working on digitalization of paper documents from 1961 to 1971, before the work became a commissioned project from the Ministry of the Environment. The data will be disseminated internationally through GBIF.

As for the archived specimens data, digitalization of label information of the skin specimens, which constitutes much of the specimens collection at the institute, was finished in the phase 2. In the phase 3 label information of egg and nest specimens will be digitalized. The data will be made GBIF compatible and will be introduced in the institute's website and will be disseminated internationally via GBIF.

As for DNA sequence data, more than 8,000 tissue samples collected in the last 10 years will be used to sequence approximately 250 species of birds that breed in Japan for their DNA barcoding.

Furthermore, we will try to sequence the DNA extracted from the specimens of extinct birds which is in the possession of the institute. As for endangered species the entire sequences of the mitochondrial genomes will be sequenced. The results will be registered in international databases.

Exploitation of New Areas of Ornithology

As for the creation of a research theme (preparation towards launching of a new international project), separate from the existing international projects, we believe that development of a new area of ornithological research will be possible by analyzing the bird specimens using modern technologies.

For an example, if the morphological data of skeletons can be extracted from skin specimens, it will be able to supplement the skeleton specimens currently in shortage worldwide. By collaborating with the areas of palaeontology and zoo-archaeology, it may be possible to create a new academic research area. CT system (*3) will be used in the research to extract a three dimensional data of skeletons from skin specimens in high precision and without destroying the specimens. We plan to conduct a research on morphological evolution of bird species.

Furthermore, the technology for easily measuring the colors of bodies and eggs will be developed. The color quantifying technologies have significantly developed in the recent years but they still have several inadequacies for them to be applied in ornithological research. By adding some technical improvements to cover the current problems and by actually applying them to bird specimens, we expect we can conduct a global study on variations in bird colors and their evolution, which could open a path to a new frontier of ornithology.

Specimens are photographed using the liquid crystal tunable filter for development of color quantification technology

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In order to achieve the two goals of 1) participation in the existing international projects and 2) preparation for establishment of a new international project、the four areas of research activities have been identified.

  1. 1. Development and disclosure of banding database
  2. 2. Establishment and publication of DNA barcoding
  3. 3. Studies on the advancement of specimens database
  4. 4. Organization of literature and publishing of the Journal of the Yamashina Institute for Ornithology

The above plan has already been approved by the Ministry of Education, Culture, Sports, Science and Technology, and will be implemented in 2009 for 56 million yen.

The overall steering and research coordination committee, equivalent to the external evaluation committee of this research, consists of Aoki Kiyoshi (Professor Emeritus, Sophia University), Endo Hideki (Professor, the University of Tokyo / Visiting Researcher, Yamashina Institute for Ornithology), Hayakawa Nobuo (Executive Commentator, Japan Broadcasting Corporation), Hayashi Yoshihiro (Professor, The University of Tokyo / Deputy Director General, Yamashina Institute for Ornithology), Hidaka Toshitaka (Former Director General, Research Institute for Humanity and Nature), Hoshi Motonori (Professor Emeritus, Tokyo Institute for Technology), Ishii Susumu (Professor Emeritus, Waseda University/ Visiting Researcher, Yamashina Institute for Ornithology), Iwatsuki Kunio (Director General, Museum of Nature and Human Activities, Hyogo), Kawanabe Hiroya (committee chairman; Director General, Lake Biwa Museum), Miyata Takashi (Advisor, JT Biohistory Research Hall), Nakamura Hiroshi (Professor, Shinshu University / President, The Ornithological Society of Japan), Ono Yuichi (Director General, Kitakyushu Museum of Natural History and Human History), Shinji Isoya (Professor, Tokyo University of Agriculture), and Wada Eitaro (Program Director, Frontier Research Center for Global Change).

(*1) GBIF: Global Biodiversity Information Facility
It aims to make the worldwide biodiversity information freely accessible by anyone through development of a distributed database network. It initially focuses on data at the levels of species and specimens but will eventually be linked to molecular/genetic or ecosystem levels in the future. It is an international science project based on the multilateral agreement by countries and international organizations.

(*2) DNA barcoding
It is a technology that enables identification of species from a very small sample by determining a short DNA nucleotide sequence from a specific gene region that reflects differences of species. There is a project called International Barcode of Life, which sequences all kinds of organisms worldwide and register in a database, and is participated by institutions and organizations around the world.

(*3) CT: computed tomography
It is a technology that produces cross-sectional or three dimensional images of an object by irradiating x-rays on the object and processing the images obtained by a computer.