A Global COE (Center of Exellence) Program

Asian Conservation Ecology
 
 
 
1. Outline of plan for establishing the COE of Asian Conservation Ecology

As a fruit of 30 years of intensive academic efforts by scientists, threats of global warming are now widely accepted as real, and requiring urgent responses by governments, scientists and the general public.  However, the deterioration of global environments caused by increasing human activities is not confined to global warming.  Together with many other changes such as decrease in the extent of forest cover and wetlands, the mass extinction of wild species, and the loss of genetic variation, the basis of our human civilization continuously has been threatened.  These changes are collectively called “biodiversity loss”.

Under the Convention on Biological Diversity (CBD), international efforts have been made to achieve by 2010 significant reduction of the current rate of biodiversity loss.  In 2008, the Group of Earth Observation Biodiversity Observation Network (GEO BON) was launched to collect and analyze data on the status and trends of the world’s biodiversity.  However, the methodology to quantify biodiversity loss at the global, regional and national scale remains underdeveloped and integrative and predictive science for global biodiversity changes must be urgently developed.

The goal of our COE-establishment plan is to develop global conservation science in which dynamic interactions among biodiversity, ecosystem function, and human activity are quantified, analyzed and modeled as a whole so that biodiversity changes in future can be projected under some plausible pathways and some actions undertaken to reduce the rate of biodiversity loss.  Towards this goal, we focus on biodiversity changes in Asia where the most serious biodiversity loss in the world is going on, including rapid loss of tropical rain forests.  The rate of forest loss in tropical Asia has now exceeded corresponding rates in tropical areas of Africa and Latin America.  Because 80% of wood used in Japan is imported, our country is largely responsible for forest loss in other countries.

The leader and a deputy leader of our COE-establishment plan, Tetsukazu Yahara of Kyushu University and Izumi Washitani of the University of Tokyo, published a comprehensive textbook entitled “An Introduction to Conservation Ecology” (Washitani and Yahara, 1996) that triggered a surge of research activities in the field of conservation biology in Japan.  Since then, scientists of Kyushu University and the University of Tokyo have played leading role in developing conservation biology in Japan.  Based on achievements of that collaboration, our COE-establishment plan aims at founding a national center of Asian Conservation Ecology, in which our research activities and graduate course will be extended from traditional conservation biology at the local and national scales to more comprehensive conservation science at the continental and global scales.

We promote the following plan of research and education to establish the COE of Asian Conservation Ecology: 1) development of cutting edge conservation science in three strategic research areas; sustainability of Asian biodiversity, restoration of Japanese biodiversity, and dynamics of eco-social systems, and 2) development of corresponding graduate programs, the Global Ecology Course, the Restoration Ecology Course, and an Integrative Program that links the two courses.

In the Global Ecology Course, graduate students will be trained to become specialists of global conservation ecology through a series of course works at Asian supersites as well as at other supersites in North and South America, Europe, Australia and Africa.  In Restoration Ecology Course, graduate students will be trained to become specialists of restoration ecology through a series of course works at some supersites in Japan where intensive restoration projects are ongoing under the collaboration of scientists, citizen, and public sectors.  Students of both courses will be trained for interdisciplinary skills including mathematical modeling, statistical analysis, computer programming, data mining, ecosystem observation, biodiversity assessment, evolutionary approaches, molecular biology and social science. Outstanding students will be invited to Integrative Program in which cutting edge research projects on Asian biodiversity changes considering complicated dynamics of eco-social systems will be promoted.

To develop conservation ecology at the global scales, we will promote our activities of research and education in collaboration with DIVERSITAS, an international multidisciplinary program of biodiversity science. In particular, we will contribute to establish the global network of GEO BON by organizing a corresponding activity in Japan (JBON). Further, Dr Yahara will be able to promote COE activites in his role as co-chair of the GEO BON working group for monitoring genetic and phylogenetic diversity. By October of 2010, when CBD COP10 will be held in Nagoya, we will provide some early results of our integrative research activities and by 2013 establish the Center of Asian Conservation Ecology.

2. Objectives, significance and prospective impacts of proposed COE

1) The disciplines to be covered by the proposed COE


The proposed COE aims at integrating biodiversity sciences, ecosystem sciences and social sciences.  It covers ecology, taxonomy, and evolutionary biology as biodiversity sciences, forest hydrology, material cycling research and environmental physics as ecosystem sciences, and environmental economy, risk assessment, and human decision making as social sciences.  Biodiversity loss and ecosystem degradation are two major aspects of environmental changes at both local and global scales.  However, there remain serious gaps between these two disciplines.  By establishing an integrated research group, we will develop new integrated research trends emphasizing biodiversity-ecosystem links.  It is critically important to understand predictive patterns of human activities and their influences upon biodiversity and ecosystems.  To deepen our understanding of this issue, we will develop eco-social system coupling models and apply them to case studies at Asian supersites, by using GIS-based state transition analyses.

2) The concepts, objectives and direction of the proposed COE


A critical challenge in today’s environmental science lies in understanding how environmental changes, such as global warming, forest decline, species loss and other trends, are mutually related and interact with each other.  To address this challenge, it is most important to integrate biological and physical approaches.  The objective of our COE plan is to promote this integration, including integrative observations at ecosystem, species and gene levels.  We will organize three research groups and corresponding graduate programs for a series of cutting-edge studies by focusing on the following strategic research areas:

(1)    Sustainability of Asian Biodiversity: This research group will focus on biodiversity in Asian countries other than Japan.  Asia is the area where both economic growth and associated biodiversity loss are most rapid in the world.  Furthermore, available data of biodiversity changes in Asia is considerably poorer than in Latin America or Africa.  Thus, it is urgently needed to develop efficient systems of monitoring biodiversity changes in Asia and to identify pathways to reduce the rate of biodiversity loss so as to make Asian biodiversity sustainable.

(2)    Restoration of Japanese Biodiversity: This research group will focus on biodiversity restoration in Japan.  Since the Nature Restoration Law was enforced in Japan in 2003, there has been a growing number of restoration projects in areas where biodiversity hasseriously deteriorated.  Those projects provide indispensable opportunities to understand dynamic interactions of biological and physical factors in ecosystems.  Under most restoration practices, it is not always easy to predict changes in ecosystem, species and genes, and it is urgently needed to develop usable technologies of ecosystem management based on the ideas of adaptive management and the precautionary principle.

(3)    Dynamics of Eco-social Systems: This research group will focus on modeling biodiversity changes.  In most areas, biodiversity is changing under the strong influence of human activities.  Thus, it is urgently needed to develop predictable models of biodiversity changes by incorporating the complex dynamics of ecological-social coupling systems.  Both analytical models and grid-based transition models are required to deepen our knowledge about the dynamics of eco-social systems.

In both the Asian Biodiversity group and the Japanese Biodiversity group, we will promote integrative biodiversity observations in a number of “supersites” where some efforts of conservation and restoration have been made. These important biodiversity observation “supersites” maintained by Kyushu University and the University of Tokyo are located in China, Vietnam, Cambodia, Thai, Malaysia and Indonesia.  In these “supersites”, we have a unique opportunity to carry out biodiversity observations integrating methodologies of remote sensing, hydrology, nutrient cycling, stable isotope, community ecology, niche modeling, phylogenetics and population genetics.  To date, few institutes are attempting to integrate biodiversity observations at all three levels of ecosystem, species and gene by using both physical and biological observation systems.  By creating a network of biodiversity observation “supersites” in Asia and carrying out integrative observations there, our COE program will establish a pioneering research hub of the world’s highest standard.  More specific plans for research activities are described in the next section (3-1). 

3) What are the most compelling reasons for establishing this COE in Japan? How can its program be expanded in the future? What makes the proposed COE exceptional and unique when compared to other education/research centers in Japan and overseas?

Japan is internationally known as a country having strong tradition of research activities in the field of ecology and evolution.  Basic theories of plant population dynamics, molecular evolution and some other critical issues in ecology and evolution have been developed by Japanese scientists.  Japan is also a center of studies for Asian biodiversity and Asian ecosystems.  From the standpoint of promoting science, great advantages for Japan are found in establishing a COE in ecology and evolution.  Furthermore, the Japanese Government has made a leading effort to develop a 10-year implementation plan for a Global Earth Observation System of Systems (GEOSS).  As a result of international efforts since 2003, the global observation system of physical environmental variables such as temperature has been greatly improved, but the observation system for biodiversity remains poorly developed.  Japan is expected to play a central role in overcoming this delay, and our COE plan will provide innovative solutions to the challenges of biodiversity change observations.

Kyushu University is known as one of the most active centers of international research activities in the field of ecology and evolution, and the University of Tokyo is known for its distinguished activities in conservation ecology.  Researchers from both universities have numerous publications in international journal including Nature and Science (see 3-3).  In particular, citations of papers published by seven researchers of the Department of Biology, Kyushu University exceed 10,000.  Kyushu University is also an Asian hub of international scientific consortia and networks. Tetsukazu Yahara, the leader of this proposal, is active in co-chairing a core project of DIVERSITAS - an international programme of biodiversity science, working as a council member of the International Organization of Plant Biosystematics, and contributing to IUCN SSC – Species Survival Commission as a Red List Authority.  Yoh Iwasa is an international leader of theoretical biology and was an editor-in-chief of two international journals; Journal of Theoretical Biology and Ecological Research.  He also serves as a Faculty Affiliate of Harvard University and has been elected as a foreign honorary member of AAAS.

As is described above (2-2), both Kyushu University and the University of Tokyo are exceptional in their activities of promoting conservation/restoration projects in many “supersites” in addition to their highly qualified activities in fundamental research of ecology and evolution.  The activities in conservation/restoration projects distinguish them from other education/research centers of ecology and evolution in Japan and overseas.  In Japan, it is well known that scientists of Kyushu University and the University of Tokyo have played a leading role in developing conservation biology since the publication of “An Introduction of Conservation Ecology” (Washitani and Yahara 1996).  At present, the two universities are playing a critical role in organizing the Japanese Biodiversity Observation Network (JBON) in collaboration with DIVERSITAS and GEO.  In April 2009, Kyushu University founded the Research Organization of Environmental Studies in East Asia, under the support of MEXT, and is going to develop institutional collaboration with some leading universities in China for promoting environmental studies in East Asia. Our COE-establishment plan is tightly linked with this Research Organization, and in the future, our program will be expanded by developing a network of leading Asian universities and research institutes. Specifically, the Center of Asian Conservation Ecology will be established by 2013.

Both Kyushu University and the University of Tokyo have a long history of graduate course education for Asian students.  Until today, a total of 115 people earned Ph.D. degrees in those graduate courses of Kyushu University corresponding to our COE program. They  are now working in 20 Asian countries as professors, research stuffs, and governmental staffs.  This human network provides us a great advantage in developing the Center of Asian Conservation Ecology.

3. Plan for research activities

1) The objectives that the research activities are expected to achieve.

More specifically, we will employ the following novel strategies to promote a series of pioneering studies on the strategic research areas described above:

Objective 1: Creating a supersite network in Asia: We will create a network including twelve “supersites” in Asian countries, and an additional ten “supersites” in Japan, where standardized and integrative observations of biodiversity changes are being carried out in association with various practices of conservation, restoration and ecosystem management.  Researchers of Kyushu University and the University of Tokyo have demonstrated unique achievements in their activities of promoting collaborative projects at many conservation/restoration “supersites”.  Examples are the Biodiversity Reserve in the new campus area of Kyushu University where we are carrying out forest ecosystem transplantation and other innovative conservation practices (Science 305: 329-330, 2004), Sado Island where we are carrying out a reintroduction project of a threatened bird, Nipponia nippon, based on restorations of river system and food webs, Kampong Thom in Cambodia where monitoring biodiversity changes in more than 200 plots of restored forest are being monitored, and Lake Tai-fu in China, where an integrated project of water quality improvement and biodiversity conservation are being carried out.  By networking those “supersites”, we will develop integrative observation systems of biodiversity changes in Asia.  We will treat “practices” at supersites as replicates of larger “experiments”. We will model the performance of “practices” as a function of ecological and social factors, and identify those factors that significantly contribute to the success of conservation/restoration practices.

Objective 2: Integrating geoinformatics with phylogenetics: We will develop biodiversity informatics by integrating GIS-based approaches with DNA sequence datasets.  GIS (Geographical Information System) has been employed to georeference distribution records and relate them with georeferenced data on climate, topology, land use and others.  Those georeferenced data have been used to develop models (e.g., bioclimatic envelope models) to predict future distribution under environmental changes such as global warming.  DNA sequences have been used to reconstruct history of differentiation and migration in various plant and animal lineages.  While the former approach considers environmental factors limiting current distribution ranges, the latter approach focuses upon history of distribution ranges.  These two approaches are complementary because distribution ranges are in most cases limited not only by current environmental variables but also by history of migration and adaptation.  However, very few efforts have been made to combine them.  By combining these approaches, we will develop models to relate land use changes (e.g., forest loss) with loss of genetic and phylogenetic diversities.  We will quantify genetic and phylogenetic diversity within and among areas at our Asian supersites, and will link to land use changes using satellite images and ground truth observations. By using these data with appropriate models, we will be able to quantify ongoing loss of genetic and phylogenetic diversities in Asia.  Based on our research in Asia, we will propose an international program for Actions of Genetic Diversity Assessment (AGenDA) in collaboration with DIVERSITAS and GEO BON.

Objective 3: Developing predictable models of biodiversity changes.  In all of the three strategies stated above, we will emphasize not only empirical but also theoretical approaches in order to develop analytical frameworks of biodiversity and ecosystem changes at various spatial scales; from local scale monitored by Field Servers to regional and continental scales monitored by remotely sensed images.  In our theoretical studies, we will use (1) statistical modeling intending to summarize and analyze empirical data, (2) physical modeling to describe fundamental structure of ecosystems, and (3) eco-social modeling to predict coupled changes of ecosystems and human systems.  Satake and Iwasa (2006) developed a model to describe coupled ecological and social dynamics in a forested landscape considering social learning of the individual decisions, and opened a way to integrate ecology and social science.  In our COE-development program, we will further develop this kind of modeling for various ecological life systems, and apply them to conservation and management actions in the areas surrounding supersites in various Asian countries.  In conservation/restoration studies at the supersites, we will make full use of spatial statistics and mapping techniques to integrate multiple factors for predicting biodiversity-ecosystem-human system changes.

2) Plan and method for achieving the above objectives.

i) Network for developing an international COE


We will collaborate with DIVERSITAS, an international programme of biodiversity science to develop international networks of cutting-edge research in biodiversity.  Tetsukazu Yahara, a leader of our COE program, is chairing one of the four core projects of DIVERSITAS in collaboration with another co-chair, Michael Donoghue of Yale University, and we therefore have a base for developing further international collaboration under the network of DIVERSITAS. DIVERSITAS involvement also assists our links to GEO BON collaborators, including NASA and IUCN. We will also collaborate with hydrologists and ecologists in Duke University and Coweeta LTER that are the international research centers of forest ecosystem research.  Tomo’omi Kumagai stayed in Duke University from 2002-2003 and he is maintaining networks with leading hydrologists.  We also have international networks of theoretical biology. Yoh Iwasa was invited to excellent institutes such as Imperial College at Silwood Park, U.K., Wissenschaftskolleg zu Berlin, Germany, International Institute for Applied Systems Analysis, Austria, Institute of Advanced Study, Princeton University, USA, and the Program in Evolutionary Dynamics, Harvard University, USA.

ii) Plans to facilitate cooperation and communication among all the participating members of the COE

Researchers who will participate in our COE program will belong to one of three units of research and graduate education; Sustainability of Asian Biodiversity, Restoration of Japanese Biodiversity, and Dynamics of Eco-social System. All three units share a common objective to integrate observations at the ecosystem, species and gene levels. All researchers will at least partly participate in collaborative studies in the Biodiversity Reserve of Kyushu University. By sharing this common field station, we will develop a tight integration of biodiversity and ecosystem studies. We will also organize cross-cutting teams to develop collaborative research in other supersites.

We will have a monthly seminar by inviting leading researchers. One invited researcher and one member of the COE program will give presentations in the monthly seminar. Most members of our COE program and most students in their labs will attend the seminar and interact with invited researchers and with each other.

Collaboration in a common field station is the most effective way to develop truly integrative research. We will hold to this principle in our COE program and we will carry out collaborative research in 10 supersites in Japan (including Biodiversity Reserve of Kyushu University), and 12 supersites in Asia. We will carry out both biodiversity and ecosystem observations in those supersites and compare findings among sites. Biodiversity observations include distribution surveys of a set of organisms (plants, bees, butterflies, ants, and beetles) based on GIS integrated with phylogenetic analyses of those organisms derived from DNA sequences. Ecosystem observations include hydrological and meteorological surveys integrated with ecological analyses of multi-species dynamics. Our program will provide the first example of well-organized study that integrates biodiversity and ecosystem studies and will trigger similar efforts in other area of the world.

3) Summary of the members’ research activities

a) List of the major research achievements that characterize the COE

Tetsukazu Yahara carried out unique research on the interaction between geminivirus and its host plants. His contributions include demography of host plants under epidemics in the field (1993, Oecologia), physiology of virus-infected leaves (1997, American Journal of Botany), molecular evolution of geminivirus (1999, Molecular Ecology), and demonstration of the earliest recorded plant virus disease (2003, Nature). He is also active in evolutionary studies of various plant reproductive systems using both ecological and molecular approaches. On the other hand, he organized a nation-wide project of extinction risk analysis for 1,549 spp of vascular plants native in Japan and utilized the database developed to the impact assessment of the Japanese 2005 World Exposition (2003, Chemosphere). Recently, he organized a biodiversity conservation project in the new campus area of Kyushu University and his project including forest ecosystem transplantation was introduced in Science (2004). He has published 91 papers in English.

Yoh Iwasa carried out theoretical studies in a broad array of ecological and evolutionary topics such as evolution of mate preferences and ornamental traits (1994, Evolution; 1995, Nature; 1998, PNAS), forest dynamics with spatial structure (1993, Ecology; 1996, Journal of theoretical Biology; 2006, Ecological Modeling), synchronized reproduction in forest trees (2002, Journal of Ecology), dynamics of cancer (2005, Nature; 2006, PNAS), coupled ecological-social dynamics (2007, Ecological Economics), evolution of human cooperation (2009, Nature) etc. He has published 227 papers in English. He will work as a deputy leader of our COE program.

Hidenori Tachida, a population geneticist, developed a nearly neutral mutation model in finite populations (1991, Genetics; 2000, Journal of Molecular Evolution), a haploid model of gene duplication (1998, Genetics) and some other important models in population genetics. He also carried out empirical studies of population genetics and molecular evolution in conifers (2002, Molecular Biology and Evolution), dipterocarps (2005, American Journal of Botany), and Lake Victoria cichlids (2006, Plos Biology; 2009, Nature). He has published 75 papers in English.

Kenichiro Shimazaki
, a plant physiologist, is a leader of research on regulation of stomatal opening. He succeeded in isolating guard-cell protoplasts from intact leaves and used it to demonstrate that activation of H+-ATPase is involved in light-induced stomatal opening (1986, Nature). He also demonstrated that phot1 and phot2 mediate blue light regulation of stomatal opening (2001, Nature) and an RNA-binding protein modulated by abscisic-acid-activated protein kinase regulates stomatal closure under water stress (2002, Nature), and protein phosphatase 1 positively regulates stomatal opening in response to blue light (2006, PNAS). He has published 85 papers in English.

Izumi Washitani is a leader of conservation biology in Japan. She carried out a series of studies on a threatened primrose; Primula shieboldii, including effects of habitat fragmentation on seed fertility (1994, Journal of Ecology ; 2000, Ecological Research), effects of density and flowering phenology on pollen flow (2006 Journal of Ecology; 2006, American Journal of Botany), genetic consequences of strong fertility selection due to pollinator loss (1996, Conservation Biology), inbreeding depression inferred from fine-scale genetic structure (2005, Molecular Ecology), intraspecific phylogeography (2004, Biological conservation) and QTL mapping of functional traits (unpublished).  She has published 85 papers in English.

Mutsumi Nishida is a specialist of molecular phylogenetics of aquatic animals such as fish and crustacean. He is well known as a leader of the MitoFish project in which he and his colleagues determined major patterns of higher teleostean phylogenies based on 100 complete mitochondrial DNA sequences (2003, Molecular Phylogenetics and Evolution). He is also active in the research of conservation genetics; he and his colleagues recently discovered an ancient native lineage of carp endemic to Japan and demonstrated cryptic large-scale invasion of non-native genotypes of common carp (2008, Molecular Ecology). He has published 136 papers in English.

Tomo' omi Kumagai primarily focuses on root-water uptake and soil moisture dynamics, and the environmental controls on transpiration and carbon and water movement in Southeastern Asian tropical forests. He has developed a stochastic carbon and water cycling model with its primary forcing term being rainfall statistics (2004, Advances in Water Resources ; 2004, 2009, Water Resourses Research ). The model was validated against his field measurements conducted in a tropical rain forest in Sarawak, Malaysia in the context of ecosystem carbon and water cycling (2005, Agricultural and Forest Meteorology ; 2006, Journal of Geophysical Research). This, among many others of his manuscripts, were among the first to report on the annual and interannual variations in water, carbon and energy fluxes above Southeast Asian tropical rainfaorest, a crucially understudied ecosystems and how these ecosystems may respond to projected shifts in rainfall. He has published 32 papers in English. 

b) List of the major scientific papers and publications

Kamiya K, Moritsuka E, Yoshida T, Yahara T, and Tachida H. 2008. High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear loci. Molecular Ecology 17: 2329-2338.
Yasumoto A. A. & Yahara T. 2006. Post-pollination reproductive isolation between diurnally and nocturnally flowering daylilies, Hemerocallis fulva and Hemerocallis citrina.  Journal of Plant Research 119:617-623.
Murayama K, Yahara T, Terachi T.  2004.  Variation of female frequency and cytoplasmic male-sterility gene frequency among natural gynodioecious populations of wild radish (Raphanus sativus L.).  Molecular Ecology 13 (8): 2459-2464.
Saunders, K., Bedford, I. D., Yahara, T., and Stanley, J.  2003. The earliest recorded plant virus disease.  Nature 422: 831.
Matsuda, H., Serizawa, S., Ueda, K., Kato, T. and Yahara, T.  2003. Assessment of the impact of the Japanese 2005 World Exposition project on the extinction risk of vascular plants.  Chemosphere 53: 325-336.

Ohtsuki, H., Y.Iwasa, and M.A. Nowak. 2009. Indirect reciprocity provides only a narrow margin of efficiency for the costly punishment. Nature 457:179-182.
Tachiki, Y. and Y. Iwasa. 2008. Role of gap dynamics in the evolution of masting of trees. Evolutionary Ecology Research. 10: 893-905.
Iwasa Y., T. Uchida, and H. Yokomizo. 2007. Nonlinear behavior of the socio-economic dynamics for lake eutrophication control. Ecological Economics 63: 219-229.
Michor, F., T.P. Hughes, Y. Iwasa, S. Branford, N.P. Shah, C.L. Sawyers, and M.A. Nowak. 2005. Dynamics of chronic myeloid leukemia. Nature 435, 1267-1270.
Iwasa, Y., F. Michor, and M. Nowak. 2004. Evolutionary dynamics of invasion and escape. Journal of Theoretical Biology 226:205-214.

Seehausen, O., Y. Terai, I. S. Magalhaes, K. L. Carleton, H. D. J. Mrosso, R. Miyagi, I. van der Sluijs, M. V. Schneider, M. E. Maan, H. Tachida, H. Imai, and N, Okada, (2008) Speciation through sensory drive in cichlid fish. Nature 455: 620-627.
Fujimoto, A., T. Kado, H. Yoshimaru, Y. Tsumura and H. Tachida (2008)  Adaptive and Slightly Deleterious Evolution in a Conifer, Cryptomeria japonica.  Journal of Molecular Evolution 67(2):201-210.
Kusumi J., A. Sato and H. Tachida (2006) Relaxation of functional constraint on light-independent protochlorophyllide oxidoreductase in Thuja.  Molecular Biology & Evolution 23 (5) 941-948.
Kusumi J. and H. Tachida (2005) Compositional properties of green-plant plastid genomes.  Journal of Molecular Evolution 60 (4) : 417-425.
Sano A. and H. Tachida,  (2005) Gene Genealogy and Properties of Test Statistics of Neutrality Under Population Growth. Genetics 169: 1687-1697.

Inoue S, Kinoshita T, Matsumoto M, Nakayama KI, Doi M, and Shimazaki K (2008) Blue light-induced autophosphorylation of phototropin is a primary step for signaling. Proceedings of National Academy of Science 105: 5626-5631
Inoue S, Kinoshita T, Takemiya A, Doi, M and Shimazaki K (2008) Leaf positioning of Arabidopsis in response to blue light. Molecular Plant 1(1):15-26 
Takemiya, A. Kinoshita, T. and Shimazaki, K. 2006. Protein phosphatase 1 positively regulates stomatal opening in response to blue light in Vicia faba. Proceedings of National Academy of Science 103: 13549-13554.
Li, J., Kinoshita, T., Pandey, S., Ng, C. K-Y., Gygi, SP., Shimazaki, K. and SM. Assmann. 2002. Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase. Nature 418: 793-797.
Kinoshita, T., Doi, M., Suetsugu, N., Kagawa, T., Wada, M. and Shimazaki, K. 2001. phot1 and phot2 mediate blue light regulation of stomatal opening. Nature 414: 656-660.

Matsuzaki, S. S-I., Nishikawa, U. Takamura, N. and Washitani, I. 2009. Contrasting impacts of invasive engineers on freshwater ecosystems: an experiment and meta-analysis. Oecologia, 158: 673-686.
Ishii, H., Kadoya, T., Kikuchi, R., Suda, S-I. and Washitani, I. 2008. Habitat and flower resource partitioning by an exotic and three native bumble bees in central Hokkaido, Japan. Biological Conservation, 141, 2597-2607.
Honjo, M., Ueno, S., Tsumura, Y., Handa, T., Washitani, I. and Ohsawa, R. Tracing the origins of stocks of the endangered species Primula sieboldii using nuclear microsatellites and chloroplast DNA. Conservation Genetics, 9: 1139-1147, 2008.
Kadoya, T., Suda, S., Tsubaki, Y. and Washitani, I. The sensitivity of dragonflies to landscape structure differs between life-history groups. Landscape Ecology, 23: 149-158, 2008.
Ishihama, F., Ueno, S., Tsumura, Y. and Washitani, I. Effects of density and floral morph on pollen flow and seed reproduction of an endangered heterostylous herb, Primula sieboldii. Journal of Ecology, 94: 846-855, 2006.

Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, Nishida M. 2008. A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces : Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification? BMC Evolutionary Biology 8: #212.
Lavoue S, Miya M, Poulsen JY, Moller PR, Nishida M. 2008. Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. Molecular Phylogenetics and Evolution 47: 1111-1121.
Mabuchi, K., Senou, H. and Nishida, M. 2008. Mitochondrial DNA analysis reveals cryptic large-scale invasion of non-native genotypes of common carp Cyprinus caprio in Japan. Molecular Ecology 17: 796-809.
Kuriiwa, K., Hanzawa, N. Yoshino, T. Kimura, S. and Nishida, M. 2007. Phylogenetic relationships and natural hybridization in rabbitfishes (Teleostei: Siganidae) inferred from mitochondrial and nuclear DNA analyses. Molecular Phylogenetics and Evolution 45, 69-80.
Hashiguchi, Y. and Nishida, M. 2007. Evolution of trace amine-associated receptor (TAAR) gene family in vertebrates: lineage-specific expansions and degradations of a second class of vertebrate chemosensory receptors expressed in the olfactory epithelium.Molecular Biology and Evolution 24: 2099-2107.
 
Kumagai, T., Yoshifuji, N., Tanaka, N., Suzuki, M. and Kume, T. 2009. Comparison of soil moisture dynamics between a tropical rainforest and a tropical seasonal forest in Southeast Asia: impact of seasonal and year-to-year variations in rainfall. Water Resources Research, 45: W04413, doi:10.1029/2008WR007307.
Kumagai, T., Tateishi, M., Shimizu, T. and Otsuki, K. 2008. Transpiration and canopy conductance at two slope positions in a Japanese cedar forest watershed. Agricultural and Forest Meteorology, 148: 1444-1455.
Kumagai, T., Aoki, S., Shimizu, T. and Otsuki, K. 2007. Sap flow estimates of stand transpiration at two slope positions in a Japanese cedar forest watershed. Tree Physiology, 27: 161-168.
Kumagai, T., Ichie, T., Yoshimura, M., Yamashita, M., Kenzo, T., Saitoh, T. M., Ohashi, M., Suzuki, M., Koike, T. and Komatsu, H. 2006. Modeling CO2 exchange over a Bornean tropical rain forest using measured vertical and horizontal variations in leaf-level physiological parameters and leaf area densities. Journal of Geophysical Research -Atmospheres, 111: D10107, doi:10.1029/2005JD006676.
Kumagai, T., Saitoh, T. M., Sato, Y., Takahashi, H., Manfroi, O. J., Morooka, T., Kuraji, K., Suzuki, M., Yasunari, T. and Komatsu, H. 2005. Annual water balance and seasonality of evapotranspiration in a Bornean tropical rainforest. Agricultural and Forest Meteorology, 128: 81-92.