Towards developing a Global Legume Diversity Assessment

A draft proposal of Global Legume Diversity Assessment - version 1.2 (August 7, 2010)

Tetsukazu Yahara (Kyushu University, Japan; co-chair of the bioGENESIS core project of DIVERSITAS; co-chair of GEO BON genetics/phylogenetics working group)

The purpose of this document

This document is drafted to describe an idea of a global legume diversity assessment and to organize a network of scientists who will play a leading role on developing the concept and implementation of the project. A document that describes further details of the concept and implementation of the project will be drafted through discussion among a network of scientists being organized.

Needs of the assessment

There are two major needs for a global legume diversity assessment. First, global biodiversity loss is now widely recognized as one of the most critical global changes (Rockstrom et al. 2009) but we do not have sufficiently reliable estimates for the rate of biodiversity loss. Among various organisms, plants support some key ecosystem services such as photosynthesis and stabilization of soil, but plant habitats such as forests and wetlands are being rapidly lost. However, it remains uncertain how rapidly we are losing plant species diversity and its values. The global legume diversity assessment project should significantly contribute to answer this fundamental question.

Second, rapid developments of genome science technologies such as new generation sequencers have enabled us to obtain genomic information much more easily even for non-model organisms (Yahara et al. 2010). Now the time is matured to extend in-depth approaches of genome science from "model organisms" such as Arabidopsis thaliana to some "model groups". To develop "model group biology", we need to establish a database of distribution, traits, phylogeny, and utility for all the species of a target group as an infrastructure of advanced research.

Brief history

Under an increasing need for assessing global biodiversity changes, GEO BON (Group on Earth Biodiversity Observation Network) is organized in February 2008 to contribute to the efficient and effective collection, management, sharing, and analysis of data on the status and trends of the world's biodiversity (GEO BON concept document; see also Scholes et al. 2009).

The bioGENESIS core project of DIVERSITAS published a bioGENESIS science plan in 2009 in which strategies and tasks of biodiversity observation using various evolutionary approaches are identified, including global genetic/phylogenetic diversity observation by coordinating advanced approaches to biodiversity monitoring and conservation practice.

In May 2010, GEO BON released a GEO BON detail implementation plan in which Working Group 1 (genetics/phlogenetics) proposed to carry out genetic/phylogenetic diversity assessments on some target groups. In the discussion to draft the detail implementation plan of Working Group 1, several plant groups such as legumes, grass, oaks, dipterocarps and conifers are considered as candidate targets.

Since then, some Japanese scientists developed a plan of Asian legume diversity assessment and discussed about this idea with Indonesian botanists in a plant ecology meeting from July 16-19, 2010, in Bali, Indonesia. In July 19-20, 2010, the bioGENESIS core project of DIVERSITAS had a Science Committee meeting in Bali, Indonesia, and agreed that legume is the best candidate as a target group for global plant diversity assessments. The idea of a global legume diversity assessment was discussed among some participants of ATBC meeting (July 22-24; Bali, Indonesia), including Tet Yahara, Dan Faith, Michael Donoghue, Lucia Lohmann, Elena Conti, Niels Raes, Stuart Davis, Cam Webb, Dedy Darnaedi, Chong Kwek Yan, Makiko Mimura, Rei'ichiro Ishii, Motomi Ito, and Tadashi Kajita.

Why legume?

Fabaceae is the third biggest family of Angiosperms, including 730 genera and 19,400 species. Compared to Asteraceae (23,000 spp) and Orchidaceae (22,000 spp), the first and second biggest family, and to Fagaceae, Dipterocarpaceae, conifers, ferns and some other candidate targets of global plant diversity assessments, Fabaceae has the following advantages.

(1) Many species are symbiotic with nodule-forming bacteria with nitrogen fixation ability, and support important ecosystem function.
(2) Legumes include many useful plants as crops, vegetables, wood, ornamental plants, and medicinal plants.
(3) Legumes include many invasive alien plants, imposing serious economic costs.
(4) Its habitat diversity is extremely high; legumes occur from tropics to arctic areas, from seashore to alpine habitats, and in rainforests, mangroves, peat swamp forests, seasonal forests, savanna, and desert.
(5) Legumes are extremely diversified in life forms, including annuals, shrubs, canopy trees, vines, and aquatic plants.
(6) Legumes are also extremely diversified in functional traits of leaves, stems, flowers, fruits and seeds. For example, seed size is extremely diversified from less than 1mm to larger than 10cm, and thus some species are efficient colonizers while others have very low dispersal ability.
(7) Seeds of legume contain a lot of unique chemicals on which a rich database is available.
(8) Legumes are mostly animal-pollinated and sensitive to pollinator loss.
(9) Legumes harbor many specific herbivorous insects and support characteristic food webs.
(10) Whole genome sequences of Medicago truncatula, Lotus japonicus and Glycine max are already determined and those of some others will be determined.

Asia as the first step

We will start the legume diversity assessment from Asia as the first step, carry out an Asian project from 2011-2015, and extend the assessment to global scale within the term of this project. There are the following reasons for us to start the assessment from Asia.

(1) The rate of forest loss in tropical Asia has now exceeded that in Latin America and is still increasing. Thus the rate of plant species loss is considered to be the most serious in tropical Asia among the world.

(2) Under GEO BON, AP-BON (Asia-Pacific Biodiversity Observation Network) is organized through three workshops held in 2009 under the financial support of the Ministry of Environment, Japan and a network of biodiversity scientists covering almost all Asian countries is well established. This is the first regional BON established for mega-biodiversity countries. Tetsukazu Yahara and Rodorigo Fuentes (ASEAN Center for Biodiversity) are chairing AP-BON. The Ministry of Environment, Japan will provide a research grant for five year term projects to develop models and tools to observe/assess biodiversity changes in Asia. The legume diversity assessment in Asia can be supported by this grant. To promote the five year project of legume diversity assessment, a kick-off meeting will be held in the summer of 2011 in Japan.

Mainly due to these reasons, we will start the assessment from Asia, but it is highly desirable to organize corresponding projects in other areas and extend the assessment project to global scale.

Tasks and goals

There are seven major tasks of the five year project of Asian legume diversity assessment.

(1) Collecting distribution records of all legume species of Asia, modeling distribution probabilities of most species, and identifying geographic patterns in species richness and endemism.
(2) Carrying out extinction risk analyses by using predicted distribution probabilities and trends of land use changes, and identifying threatened taxa and hotspots of threats.
(3) Determining phylogenies of most legume species of Asia, calculating phylogenetic diversity per map grid, and identifying hotspots of recent speciation.
(4) Developing a database of functional traits for Asian legume species, elucidating relationships among species diversity, phylogenetic diversity and functional diversity, and assessing functional diversity loss in association with species/phylogenetic diversity loss.
(5) Developing a database of traditional use of Asian legume species by local people and assessing values of loss in association with species/phylogenetic/functional diversity loss.
(6) Determining within-species genetic/phylogenetic structures for some wild species and assessing genetic changes under various human impacts. Target species includes critically endangered species, invasive alien species, wild relatives of commercially important species, and others (see GEO BON detail implementation plan).
(7) Developing genetic markers to study functional major genes associated with local adaptation and applying those markers to some particular species of conservation interest.
The goal of the project is to demonstrate how species/phylogenetic/functional diversity of legumes is valuable for human beings and how threatened the valuable legume diversity is. Based on this documentation, we will develop some proposals for conservation and sustainable use of legume diversity.

Notes on tasks

(1) Distribution records of all Asian legume species will be obtained from herbarium specimen records, plot data, and additional field works. Those data have unique advantages and disadvantages. Herbarium specimen records provide most extensive distribution data available now, but it provides only presence records. Plot data obtained from ecological studies can provide presence/absence data although we must be careful about absence of rare species because plot studies usually cover a small fraction of regionally rare species. Plot data is also valuable in that it usually provide abundance data. However, plot data usually cover only tree species and mostly lack records of herbaceous species. Additional field works in data-poor areas and/or high endemism areas are critically important to improve predictable power of distribution models, but those are time-consuming and costly. Undoubtedly, our data-collecting strategy is optimized by integrating advantages of all three datasets.
Utility of georeferenced herbarium specimen records is well documented by Raes et al. (2009); they developed distribution models for 2,273 species belonged to 102 plant families using 44,106 records of Borneo and successfully identified some centers of endemism. The National Herbarium of the Netherlands has already digitized a large number of Asian plant specimen records using BRAHMS. Herbarium at FRIM, Malaysia has also digitized 185,000 specimen records using BRAHMS over past 15 years (Guan, pers. com.). Digitizing projects are going on in some other herbaria including Indonesia and Thailand. As for Chinese plants, Chinese Virtual Herbarium provides digitized information of specimen records in major Chinese Herbaria. However, most specimen records are not yet georeferenced, and it is necessary to georeference them using label records.
Field works will be made to re-survey previously established plots and to obtain additional distribution records in areas neighboring plots, high endemism areas under high rates of habitat loss, and data-poor area where endemic species are expected to occur. In these field works, extensive transect surveys will be made as in Yaku Island where presence/absence of most vascular plant species are recorded in 270 transects of 100m x 4m (Yahara et al. unpublished).

(2) In some countries of SE Asia, a lot of forest plot data are available. In Indonesia, for example, more than 2,000 forest plots have been placed in the field (Simbolon, pers. com.). Forest plots are already converted to agricultural land in some areas, once logged but recovering in other locations, and protected but suffering various human impacts in many other cases. Those plots provide valuable data to determine sensitivity of each species to logging and other human impacts and are helpful to estimate rates of species loss, if those are re-visited and re-surveyed. By integrating ground-truth observations within and around plots with time-series records of satellite images, we will determine the rate of land use change and the decline rate of each species under land use change. Time-series analyses of satellite images will be made by a remote sensing team directed by Rei'ichiro Ishii. For extinction risk analysis of threatened species, we will modify the methods described in Yahara et al. (1998) and Matsuda et al. (2003).

(3) For phylogenetic studies, a group of researchers are actively working to improve our knowledge of legume phylogeny; directory of those researchers is available on the following website, although information of some researchers including Tadashi Kajita (Chiba University, Japan) is not updated: Legume "Phylo-informatics" dbase. A whole family tree will be used to select 100 EDGE species. Dan Faith is planning to revise the method to determine EDGE scores.

(4) For functional traits, the TRY initiative jointly headed by IGBP, QUEST, DIVERSITAS and the Organismic Biogeochemistry Group at Max Plank Institute for Biogeochemistry developed a global database of plant trait data in which more than 2,400,000 trait records have been compiled, including legume trait records. Bradshaw et al. (2008) developed a database providing information on range size, habitat and various functional traits including life history, growth habit, height, presence of armaments, presence of hairs, length of the smallest leaf unit, floral display, presence of hooks on the fruit, fruit dehiscence and seed size.

(5) For traditional use of various plants including legumes, PROSEA (Plant Resources of South East Asia), an international cooperative program with the main goal of documenting information on plant resources in South East Asia, published a series of handbooks for useful plants in which a large amount of data have been compiled.

(6) As for determining within-species genetic/phylogenetic structures, wild soybean is one of the best candidate targets. Tingshuang Yi in Kunming Institute of Botany is working on Chinese, Korean and Japanese populations of Glycine max. Makiko Mimura of Kyushu University is comparing genetic/phylogenetic structures between Lotus japonicus and L. corniculatus, a pair of native and introduced species in Japan.

(7) As for genomic research of legumes, a link page is available at the following site: Links to legume genomics databases and resources; an additional site is Lotus japonicus DB.


Bradshaw CJA, Giam X, Tan HTW, Brook BW, and Sodhi NS. 2008. Threat or invasive status in legumes is related to opposite extremes of the same ecological and life-history attributes. Journal of Ecology 96: 869-883.
Matsuda H, Serizawa S, Ueda K, Kato T, and Yahara T. 2003. Assessing the impact of the Japanese 2005 World Exposition project on vascular plants' risk of extinction. Chemosphere 53: 325-336. Pdf
Raes N, Roos MC, Slik JWF, van Loon EE, and ter Steege H. 2009. Botanical richness and endemicity patterns of Borneo derived from species distribution models. Ecography 32: 180-192.
Rockstrom J. et al. 2009. A safe operating space for humanity. Nature 461: 472-475.
Scholes RJ, et al. 2009. Toward a global biodiversity observation system. Science 321: 1044-1045.
Yahara, T., Kato, T., Inoue, K., Yokota, M., Kadono, Y., Serizawa, S., Takahashi, H., Kawakubo, N., Nagamasu, H., Suzuki, K., Ueda, K., and Kadota, Y. 1998. Red list of Japanese vascular plants: summary of methods and results. Proceedings of Japanese Society of Plant Taxonomists 13: 89-96. Pdf
Yahara T., Donoghue M, Zardoya R, Faith D. and Cracraft J. 2010. Genetic diversity assessments in the century of genome science. Current Opinion in Environmental Sustainability 2: 43-49.

Revision history

July 31, 2010: version 1.1 released. August 7, 2010: Bradshaw et al. (2008) is cited in Notes on Task (4). @



The following reserachers replied to an invitation to the project and are registered as project team members. @







- Bean bag

- International Legume Database and Information Service (ILDIS)

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