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Table of Content
    Volume 18 Issue 5
    20 September 2010

    Biodiversity Informatics is a new and rapid developing branch of crossing disciplines, which improving our understanding of global and local biodiversity by using the theory and methods of informatics. Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EOL) and Catalogue of Life (COL) are excellent types in this field. In this issue, we published six papers on Biodiversity Informatics as a focused subject so as to introduce the major contents, cutting edge progress and appl

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    Special Issue
    Progress in Biodiversity Informatics
    Lisong Wang, Bin Chen, Liqiang Ji, Keping Ma
    Biodiv Sci. 2010, 18 (5):  429-443.  doi:10.3724/SP.J.1003.2010.429
    Abstract ( 3431 )   PDF (401KB) ( 5327 )   Save
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    Biodiversity Informatics is a young and rapidly growing field that brings information science and technologies to bear on the data and information generated by the study of biodiversity and related subjects. Recent years, biodiversity informatics community has made an extraordinary effort to digitize primary biodiversity data, and develop modelling tools, data integration, and county/regional/global biodiversity networks. In doing so, the community is creating an unprecedented global sharing of information and data produced by biodiversity science, and encouraging people to consider, survey and monitor natural biodiversity. Due to success of several international biodiversity informatics projects, such as Species 2000, Global Biodiversity Information Facility, Barcoding of Life and Encyclopedia of Life, digitized information on species inventories, herbarium specimens, multimedia and literature is available through internet. These projects not only make great contributions to sharing digitized biodiversity data, but also in prompting the implementation of important biodiversity information standards, such as Darwin Core, and in the establishment of regional and national biodiversity networks. These efforts will facilitate the future establishment of a strong information infrastructure for data sharing and exchange at a global scale. Besides focusing on browsing and searching digitized data, scientists should also work on building data mining and modeling, such as MAXENT for Ecological Niche Modelling and LifeDesk for taxonomist’s knowledge management. At the same time, the idea of citizen sciences gains popularity showing us the benefit of the public working closely with the scientific community in completing internet-based biodiversity informatics activities. Therefore, biodiversity informatics has broad prospects, and is helping to build strong facilities that will aid in implementing the goals set by Global Plant Conservation Strategy and related international treaties, resolving biodiversity crises and the management of biodiversity resources in global climate change scenarios.

    Experience and strategy of biodiversity data integration in Taiwan
    Kwangtsao Shao, Kunchi Lai, Yungchang Lin, Chihjen Ko, Han Lee, Lingya Hung, Yuehchih Chen, Leesea Chen
    Biodiv Sci. 2010, 18 (5):  444-453.  doi:10.3724/SP.J.1003.2010.444
    Abstract ( 4205 )   PDF (702KB) ( 2939 )   Save
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    The integration of Taiwan’s biodiversity databases started in 2001, the same year that both the Digital Archives Program (later renamed Taiwan e-Learning and Digital Archives Program; TELDAP) and Biodiversity Action Plan were launched and Taiwan joined the Global Biodiversity Information Facility (GBIF) as an Associate Participant. In 2002, Academia Sinica began the creation of the “Catalog of Life in Taiwan” database (TaiBNET). Taiwan’s node of GBIF, TaiBIF, established in 2004, integrates Taiwan’s biodiversity data and shares it with the global community. Both TaiBNET and TaiBIF have broken through the barrier of Intellectual Property Rights and can collect and integrate data accumulated by TELDAP’s various sub-projects. However, raw data, especially those on ecological distribution, generated by different agencies or non-TELDAP projects are still dispersed due to parochialism. A cross-agency committee was thus established in Academia Sinica in 2008 to formulate policies on data collection and integration, as well as mechanisms to increase public availability of data. Any commissioned project will hereafter include these policy requirements in the contract. The results of TaiBIF’s efforts over the past six years, though not perfect, can provide some information and insights for others to reference or replicate.

    Establishment and application of National Crop Germplasm Resources Infrastructure in China
    Yongsheng Cao, Wei Fang
    Biodiv Sci. 2010, 18 (5):  454-460.  doi:10.3724/SP.J.1003.2010.454
    Abstract ( 2918 )   PDF (917KB) ( 3206 )   Save
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    Crop germplasm resources are a key component of biodiversity, and can serve as a material basis for crop breeding and agroproduction. For a long time, ununified standards, widely-scattered germplasm storage, and weak information network infrastructure have restricted the sharing and utilization of crop germplasm resources in China. In order to overcome these problems, the concept and architecture of a program called the National Crop Germplasm Resources Infrastructure (NCGRI) were proposed. The NCGRI is a virtual organization which brings together crop germplasm resources from the national long-term genebank, the national duplicate genebank, the national medium-term genebank, the national field genebank, and the national germplasm information center. The principles and methods for establishing a technical standard system were elaborated. Complete with descriptor lists, a data dictionary, and data quality control standards, the group established a technical standard system for 110 crops. A protocol for sample sharing that is driven by information sharing was put forward. The national crop germplasm resources database with 390,000 accessions and the Chinese Crop Germplasm Resources Information Network (http://www.cgris.net/) were established as repositories. Finally five service-modes including routine service, field display services, targeted services, demand for services, and guide services were created.

    PSDS (predictive species distribution system) 2.0: a system based on GIS and multiple models for predicting potential distribution of species
    Congtian Lin, Liqiang Ji
    Biodiv Sci. 2010, 18 (5):  461-472.  doi:10.3724/SP.J.1003.2010.461
    Abstract ( 2896 )   PDF (623KB) ( 3957 )   Save
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    Herein, we have proposed and implemented a predictive species distribution system (PSDS) based on GIS (Geographic Information Systems) and using multiple models, according to the situation in the field of species habitat modeling. The new system (PSDS 2.0) was developed from PSDS1.0, originally initiated by our research group. We introduced three models into PSDS 2.0, including a mahalanobis distance model (MD), an environmental envelope plus limiting factor model (EELF), and a support vector machine (SVM) model. In this paper, we describe the implementation of the system and introduce the main functions in detail. In order to compare and evaluate results from different algorithms, an iterative cross-validation technique has been implemented in PSDS 2.0, which also facilitates the selection of suitable algorithms for different sample data. A function for flexibly dealing with pseudo-absences has been incorporated into presence-absence models. A GIS interfaces with the software for data preparation and further analysis of the model results. We also present a case study using the Reeve’s pheasant, Syrmaticus reevesii, as a practical application to introduce the entire modeling process. The performance of all model types is compared within this unified system.

    Architecture and implementation of the biodiversity digital library
    Zheping Xu, Jinzhong Cui, Fenghong Liu, Zhaogai Wang, Qiaoling Li
    Biodiv Sci. 2010, 18 (5):  473-479.  doi:10.3724/SP.J.1003.2010.473
    Abstract ( 2077 )   PDF (989KB) ( 2695 )   Save
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    Biodiversity research needs a digital library on multi-source data. Biodiversity digital library,based on the virtual community, has similar features as digital libraries in data types, storage requirement and sharing methods. On the other hand, it has distinct features in terms of data mining and application. Based on an investigation of related digital library projects and cooperation with the Biodiversity Heritage Library and Internet Archive, we summarize the types of literature data in some kinds of digital libraries and briefly introduce Dublin Core and TaxonX standards which will be applied in the construction of the biodiversity digital library. Then, the present architecture of the biodiversity digital library, composed of data aggregation models and data processes, conversion and translation models and service models, is proposed in order to integrate multi-source data, construct the virtual community and provide specific data service to external web sites. Part of the implemented information system is demonstrated, and then some problems like copyright, OCR (optical character recognition) and the extension of massive data sets are discussed.

    On the architecture of biodiversity e-Science infrastructure in China
    Zheping Xu, Jinzhong Cui, Haining Qin, Keping Ma
    Biodiv Sci. 2010, 18 (5):  480-488.  doi:10.3724/SP.J.1003.2010.480
    Abstract ( 2777 )   PDF (279KB) ( 4429 )   Save
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    Considering analyses of the development of biodiversity informatics techniques, the introduction of related international biodiversity e-Science infrastructure and previous similar achievements, we suggest and describe a biodiversity e-Science infrastructure of China based on SOA and ISO 19119 Standards. Moreover, the major steps in construction of the biodiversity e-Science infrastructure are also introduced, including strong coordination and organization, data standardization and extension, data storage and computation, ontology and semantic web development, thematic analysis and modeling, and service standardization. This architecture can provide references for future construction of biodiversity e-Science infrastructure in China.

    Spatial and temporal patterns of natural forest soil seed banks on Tiantong Mountain
    Binjie Ge, Yongchuan Yang, Hongqing Li
    Biodiv Sci. 2010, 18 (5):  489-496.  doi:10.3724/SP.J.1003.2010.489
    Abstract ( 2882 )   PDF (365KB) ( 2729 )   Save
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    Soil seed bank represents a pool of potential species for a plant community. We analyzed spatio- temporal patterns of natural forest seed banks on Mt. Tiantong, a typically hilly region in East China. Eight micro-landform units, i.e., second and third crest slopes, higher-, middle- and lower-upper sideslope, lower sideslope, foot slope, and flood terrace were used as classes in our analyses. Seeds were identified from a total of 1,960 samples collected in September 2008, December 2008, March 2009 and June 2009. The results are summarized as follows: (1) The total number of viable seeds was 5,024 and 68 taxa were identified, among which 65 species were identified to species level from the samples. Among these identified species 48 were present in the above-ground vegetation and the Czekanowski community similarity was 0.45. Deciduous broad-leaved trees and evergreen broad-leaved sub-canopy trees were the main components of soil seed banks according to the number of seeds and species. (2) The reserves on crest slopes and lower hillside areas were higher than those on the upper sideslopes (H-US, M-US and L-US). Carpinus viminea and Eurya loquaiana dominated in nearly all the micro-landforms. Otherwise, evergreen trees such as E. muricata, Ilex buergeri, Symplocos heishanensis and S. setchuensis were the dominant species in upper hillside areas, while deciduous trees such as Choerospondias axillaris, Acer olivaceum, Celtis vandervoetiana dominated in lower hillside areas. (3) Reserves of four vertical soil layers varied in size, with the peak at 0–2 cm soil layer, followed by 2–5 cm soil layer and 5–10 cm soil layer, while those in the litter layer were the smallest. (4)The soil seed banks showed seasonal variation, with the peak of reserves found in December 2008, followed by March 2009, September 2008 and June 2009 in descending order.

    Phenotypic variation and covariation among natural populations of Arabidopsis thaliana in North Xinjiang
    Lei Li, Tong Liu, Bin Liu, Zhongquan Liu, Langming Si, Rong Zhang
    Biodiv Sci. 2010, 18 (5):  497-508.  doi:10.3724/SP.J.1003.2010.497
    Abstract ( 2804 )   PDF (671KB) ( 2444 )   Save
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    Phenotypic traits of the natural Arabidopsis thaliana population represent its adaptation in natural environments. Comparison of phenotypic traits among different populations can provide important clues for understanding phenotypic variation and formation processes of A. thaliana. It is an important aspect that cannot be ignored for phenotypic adaptation and evolution of natural A. thaliana populations. We investigated nine phenotypic traits of 10 A. thaliana populations located in the northern Tianshan, Altai, and Tarbagatay mountains of Xinjiang, and compared variations in phenotypic traits in natural conditions at micro-, local- and regional-scales. Our results showed that different traits respond differently to environmental changes. Plant height, plant weight, root weight, root length, single fruit weight and fruit dehiscence force differed among populations at the three scales. However, branching number and fruit length did not differ among populations with low phenotypic differentiation coefficients. Plant weight, root weight and fruit number per plant all showed a consistent integration pattern at different scales, potentially reflecting the importance of physiological functional integration in A. thaliana. These three phenotypic characteristics also exhibited obvious adaptation to local environment. At the same time, we found that the extent of integration of phenotypic traits varied between local and regional scales. Cluster analysis showed that different populations from the same region grouped together, further showing that the phenotypic traits of A. thaliana were strongly influenced by the micro-scale environmental factors. Mantel test showed that the variations of plant height, plant weight, root weight, single fruit weight, fruit length and fruit dehiscence force significantly correlated with geographic distance, while the variations of branch number and root length did not. We therefore concluded that phenotypic variations of A. thaliana were strongly affected by the microscale environmental factors. However, not all the phenotypic traits were associated with the original habitat climate.

    Genetic diversity in Sclerotinia sclerotiorum assessed with SRAP markers
    Biyun Chen, Qiong Hu, Christina Dixelius, Guoqing Li, Xiaoming Wu
    Biodiv Sci. 2010, 18 (5):  509-515.  doi:10.3724/SP.J.1003.2010.509
    Abstract ( 2495 )   PDF (403KB) ( 2724 )   Save
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    Assessing the genetic diversity of Sclerotinia sclerotiorum isolates from different eco-geographical regions and host plants is crucially important for understanding the evolution of this fungal pathogen and its control. We detected DNA polymorphism of 76 S. sclerotiorum isolates from different regions and host plants using sequence-related amplified polymorphism (SRAP) markers. A total of 260 scorable fragments were identified with seven SRAP primer combinations; among them 114 were polymorphic loci (43.85%). UPMGA (Unweighted Pair Group Method with Arithmetic Mean) indicated that the dendrogram consisted of four groups, which included 54, 18, 2, and 2 isolates, respectively, when the genetic similarity coefficient was 0.64. Little genetic difference was identified among the isolates from different host species by cluster and principal component analyses. AMOVA (Analysis of Molecular Variance) revealed that the percentage of variation among populations differed by geographical region (24.8%, P<0.001) and by ecological region (18.8%, P<0.001), but variation among populations of different host plants was not different than expected at random (2.4%, P = 0.8673). One of our most significant results was that S. sclerotiorum isolates on rapeseed plants from winter and spring ecological regions can be divided into two clusters, and that genetic diversity in isolates of spring rapeseed ecological regions was higher than that of winter rapeseed ecological regions.

    Preliminary investigation on function recognition and image perception in public upon botanical gardens
    Hai Yan, Jin Chen, He He
    Biodiv Sci. 2010, 18 (5):  516-522.  doi:10.3724/SP.J.1003.2010.516
    Abstract ( 2861 )   PDF (234KB) ( 3191 )   Save
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    By providing various educational programs, botanical gardens (BGs) can play significant roles in promoting biodiversity conservation. At the same time, how well the public recognizes the function of BG’s and the image the public forms of BG’s may influence BGs’ educational function. In this study, we selected one research botanical garden (Xishuangbanna Tropical Botanical Garden (XTBG)), one city garden (Hangzhou Botanical Garden (HZBG)) and one forest park (Wild Elephant Valley Park (WEVP)), located in the same area as XTBG, and we explored how the public’s function recognition and image perception differed. The main results were as follows: (1) For both XTBG and HZBG, visitors showed their significant acceptance of the statements that “BG is a place for germplasm collection and preservation”, “BG is a place to enhance public environmental awareness”, “BG is a professional agency for biodiversity conservation”. For XTBG as a research botanical garden, the statements for “XTBG is a research institution” and “XTBG is a place providing professional training” were also supported by the interviewees; (2) XTBG and WEVP showed differences in most descriptors of the function recognition; (3) All the three sites were recognized as “fresh air and pleasant environment”, “experience unique animals and plants”, “beautiful landscape”, “enjoy nature”. Furthermore, for the statement “It is a place for improving scientific knowledge” received the highest support at XTBG and the least support at WEVP. The study provides relevant information for improving BGs’ public image and enhances their educational function for biodiversity conservation.

    Mitochondrial DNA D-loop sequence analysis and population rejuvenation of Hainan gibbons (Nomascus hainanus)
    Zhigang Li, Fuwen Wei, Jiang Zhou
    Biodiv Sci. 2010, 18 (5):  523-527.  doi:10.3724/SP.J.1003.2010.523
    Abstract ( 2710 )   PDF (405KB) ( 2947 )   Save
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    The Hainan gibbon (Nomascus hainanus) is one among the most endangered primates globally according to Critically Endangered List of IUCN. However, there has been no report on its genetic information and the difficulties of its population restoration. This study represents the first time survey of genetic diversity using mitochondrial D-loop sequences from faecal sampling of six individuals within one group. Five variable sites were detected in the 202 bp D-loop sequences and 4 haplotypes were defined. The haplotype diversity (h) and nucleotide diversity (π) were 0.6000 and 0.00829, respectively, meaning the genetic diversity was low. Furthermore, this critically endangered species also face other threatening factors, such as small population size, biased sex ratio and low habitat quality.


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