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Table of Content
    Volume 20 Issue 2
    20 March 2012

    The concave-eared frog (Odorrana tormota), a rare frog species endemic to eastern China, is the first amphibian confirmed to possess ultrasound communication capability. Currently, the existing populations of the species are sporadically distributed in Mt. Huangshan and adjacent regions. Li et al. (for details see pages 184–192 of this issue) found that although Chinese concave-eared frog exhibits a restricted distribution, the species displays rich diversity at the B loci compared to other Ranidae species. It was deduced the MHC diversity may be maintained by the mechanisms such as positive selection and across-species evolution. (Photographed by Junxian Shen)

    How did biodiversity come about?
    Hongzhi Kong
    Biodiv Sci. 2012, 20 (2):  117-118.  doi:10.3724/SP.J.1003.2012.02091
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    Ornithological research: past twenty years and future perspectives in China
    Yong Wang, Zhengwang Zhang, Guangmei Zheng, Jianqiang Li, Jiliang Xu, Zhijun Ma, Atilio Luis Biancucci
    Biodiv Sci. 2012, 20 (2):  119-137.  doi:10.3724/SP.J.1003.2012.19175
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    To understand recent trends in the development of global ornithological research, compare these with related trends and patterns in China, and provide suggestions for future directions for Chinese ornithological research, we conducted a literature review of ornithology-related publications from 1991 to 2010 using reference database: Web of Science. We reviewed many publications and other information and provide here a summary of the trends in publication quantity and quality, major research areas, major research institutions, and individual contributions of ornithologists in the world and in China. The number of China’s ornithological professionals increased about ten times during the period, and avian-related publications in professional journals increased about 25% annually. Chinese ornithologists were recognized for their advancements in paleontology, pheasant and crane conservation, avian evolution, and applications of molecular technology to systematics. Compared with developed countries such as USA, UK, Germany and Canada, China is still behind in the quantity and quality of ornithological research and publications. In the future, we recommend that Chinese ornithologists pay more attention to studies on avian life history, the impacts of climate change and urbanization on birds, avian conservation and protection, bird migration and connectivity, research methodology improvement, research team training and multidisciplinary collaborations, long-term research and monitoring system establishment, and international cooperation.

    Assessment and management of biosafety in synthetic biology
    Zhengjun Guan, Lei Pei, Markus Schmidt, Wei Wei
    Biodiv Sci. 2012, 20 (2):  138-150.  doi:10.3724/SP.J.1003.2012.13205
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    While having developed into one of the most dynamic fields of the life sciences, synthetic biology may pose potential risks to the environment and human health. Based on current national and international risk assessment methods and current regulation of synthetic biology, we reviewed risk assessment in relation to synthetic biology’s research subfields (such as DNA-based biocircuits, minimal genome, protocells and chemical synthetic biology), its relation with biosafety engineering, its effect on ELSI (Ethics, Legal and Social Implications) and recent biosecurity challenges, such as biopunk (or biohackery), garage biology, do-it-yourself biology and bioterrorism. Additionally, we investigated existing strategies for management of synthetic biology research, focusing on self-regulatory or technology-focused methods and using the 5P (the principal investigator, the project, the premises, the provider of genetic material and its purchaser) strategy focusing in five different policy intervention points. Furthermore, we reviewed the current research and development of synthetic biology and its current biosafety regulations in China. Finally, we recommended management strategies to guide future research in synthetic biology with necessary amendments, including the establishment of regulations with a core of safety assessment, synthetic biology-specific good laboratory practice guidelines, and arguments for the reinforcement of internal regulation at the institution level and more active public outreach efforts for biosafety.

    Point pattern analysis based on different null models for detecting spatial patterns
    Xinting Wang, Yali Hou, Cunzhu Liang, Wei Wang, Fang Liu
    Biodiv Sci. 2012, 20 (2):  151-158.  doi:10.3724/SP.J.1003.2012.08163
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    Understanding spatial distribution patterns has been a central focus of plant ecology since its inception. Spatial patterns of individuals within populations are closely linked to processes; determining these underlying processes remains a major objective of ecological research. Spatial patterns are often determined using a point pattern, a data set consisting of a series of mapped point locations within a study area. The simplest and most widely used null model for analyzing point patterns is the complete spatial randomness (CSR) model. In fact, other null models are rarely used. This paper aims to provide guidance to ecologists when quantifying the underlying processes responsible for spatial patterns of ecological phenomena using point patterns and null models. Photography orientation was used to estimate the point pattern of Leymus chinensis in different restored successional stages in a typical steppe, and complete spatial randomness, Poisson and double-cluster processes were used to analyze spatial patterns of L. chinensis based on this data set. In the early stages of succession, the distribution of L. chinensis fit well with the nested double-cluster process for all scales in the community block of 10 m×10 m. Over time, the distribution fits better with the Thomas process at all scales. This ecological succession phenomenon may be induced by intra-specific competition, but cannot be explained by density interactions. Population territory density could possibly explain the phenomenon. Our study is an important example of successful analysis of population spatial patterns using point patterns and complex null models.

    Original Papers
    Coexistence mechanisms of evergreen and deciduous trees based on topographic factors in Tiantong region, Zhejiang Province, eastern China
    Yubin Xie, Zunping Ma, Qingsong Yang, Xiaofeng Fang, Zhiguo Zhang, Enrong Yan, Xihua Wang
    Biodiv Sci. 2012, 20 (2):  159-167.  doi:10.3724/SP.J.1003.2012.09242
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    The zonal vegetation of subtropical regions in China is recognized as the evergreen broad-leaved forest (EBLF), a forest that usually contains many deciduous tree species. Preliminary investigation of a 20-ha plot at Tiantong (East China) showed that the proportion of deciduous trees reached 52.6%. How do these evergreen and deciduous trees coexist? Up till now, this question lacks a sufficient answer. Evergreen and deciduous tree species often differ in ecological habits, and this niche differentiation may be manifested in distinct habitat preferences. These habitat differences may be an important point in explaining the mechanisms by which these two groups coexist. To test this hypothesis, on the basis of the aforementioned investigation at Tiantong 20 ha plot, 55 evergreen and 42 deciduous tree species with abundance more than 20 individuals were selected for analysis. Canonical Correspondence Analysis (CCA) was used to explore the influence of topographic factors on spatial distribution, and torus-translation tests were employed to test the significance of the species-topography (elevation, convexity, and slope) association. Results were as follows: (1) CCA analysis showed that the three topographic factors (elevation, convexity and slope) explained 19.2% of the distribution of evergreen trees and 7.0% of that for deciduous trees. (2) 16.4% of the 55 evergreen trees and 28.6% of the 42 deciduous trees showed a significantly positive association with the valley habitat, and the proportion of negative association with the valley habitat was 40% and 7% respectively; 41.8% evergreen trees and 4.8% deciduous trees showed a significantly positive association with the ridge habitat, and the proportion of negative association with the ridge habitat was 10.9% and 47.6% respectively; 16.4% evergreen trees and 42.9% deciduous trees were positively associated with the disturbed habitat. Our results showed that topographic factors significantly influence the distribution of evergreen and deciduous trees in the Tiantong plot, and this influence seems greater for evergreen trees. Evergreen and deciduous trees generally showed opposite trends in habitat preferences, especially in valley and ridge habitats. This indicates that habitat partitioning may be a major mechanism allowing the coexistence of evergreen and deciduous trees, and that the niche theory, to some extent, may be sufficient in explaining species diversity maintenance in subtropical evergreen forests.

    Impacts of forest logging on the species diversity of endemic seed plants from Hainan Island
    Han Xu, Yide Li, Tushou Luo, Dexiang Chen, Mingxian Lin, Huai Yang
    Biodiv Sci. 2012, 20 (2):  168-176.  doi:10.3724/SP.J.1003.2012.09169
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    Endemic seed plants are important floral components in tropical rainforests, and are often sensitive to human disturbance. However, few reports exist of the impacts of forest logging on these species. In this study, based on surveys of 164 quadrats of 25 m×25 m in Jianfengling, Hainan Island, the species composition and relationships between species richness of Hainan endemic seed plants and the total plant species richness were analyzed. Each of the 164 quadrats was grouped into one of three forest types, including old-growth, selectively logged and clear-cut forests. Then changes in species diversity were studied by comparing species-area relationships, cumulative species-individual relationships and species abundance distributions for the Hainan endemic seed plant species among the three forests types. Results highlighted the abundance and diversity of endemic seed plant species in Jianfengling. We found 158 species which acount for 40% of all endemic seed plant species found on Hainan Island, including 98 woody species (excluding lianas). Fifty-two woody endemic seed plant species (excluding lianas) from Hainan Island were recorded in the 164 quadrats; 53% of all woody endemic seed plant species in Jianfengling. Among them, Lauraceae, Fagaceae and Rubiaceae are dominant families. The richness of the woody seed plant species endemic to Hainan Island was linearly correlated with the total plant species richness in the quadrat. After forest logging, the number of woody endemic seed plant species appears to increase slightly, especially in selectively logged forests. However, the woody endemic seed plant species that appear to increase post-logging only occur in 1-2 quadrats and have relatively small and unstable populations, and may therefore disappear during forest succession. On the other hand, some endemic seed plant species still have medium populations after logging, such as Nephelium topengii, Madhuca hainanensis and Castanopsis jianfenglingensis.

    Assessment of in situ conservation of 1,334 native orchids in China
    Weihua Qin, Mingkang Jiang, Wanggu Xu, Zhaohe He
    Biodiv Sci. 2012, 20 (2):  177-183.  doi:10.3724/SP.J.1003.2012.07108
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    We assessed the status of 1,334 Chinese orchids species in terms of in situ conservation based on analysis of orchid distribution data from 543 nature reserves. Based on the number of nature reserves the orchid species have been recorded, combined with expert consultant, we determined six conservation catagories, i.e., effective conservation, better conservation, general conservation, less conservation, unknown, and not evaluated. Our results indicate that 676 orchids are currently protected by nature reserves, accounting for 51.9% of total species, and that 626 orchids (46.9%) are not found in nature reserves. In addition, 32 orchids distributed only in Hongkong, Macao and Taiwan areas were not evaluated in this paper, accounting for 2.4% of total species. Based on our assessment, we herein discuss the main problems facing orchid conservation including field survey deficiencies, lack of attention, and low rates of protecting species through in situ conservation in China. We put forward five suggestions: (1) promoting research on and monitoring of orchids; (2) increasing awareness and protection of orchids in China; (3) prioritizing the construction and design of nature reserves for orchid protection; (4) regulating biotic surveys of nature reserves through enforcement of a unified standard; and (5) regular assessment of the effectiveness of orchid conservation in China.

    Polymorphism of exon 2 of MHC Class II B gene in the Chinese concave- eared torrent frog (Odorrana tormota)
    Fang Li, Yilin Shu, Hailong Wu
    Biodiv Sci. 2012, 20 (2):  184-192.  doi:10.3724/SP.J.1003.2012.09211
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    Currently, amphibians are experiencing global population decline, and it is believed that several amphibian mass extinction events were caused by environmental pathogens (such as chytrid fungus). Major histocompatibility complex (MHC) genes play a critical role in the course of immune response in all jawed vertebrates. MHC gene is considered to be one of the best candidates to analyze animal’s adaptive evolution because its polymorphisms are usually associated with resistance or susceptibility to animal diseases. Here, we report our preliminary research on the allelic diversity of MHC class II B gene from the Chinese concave-eared frog (Odorrana tormota), a species endemic to eastern China. We initially amplified a 180-bp fragment of MHC II exon2 gene in O. tormota using published polymerase chain reaction primers. Based on these results, we successfully obtained sequences of the gene’s flanking regions using a ligation-mediated PCR method. After splicing, we obtained a sequence with length of 2,030 bp including whole exon2 and partial sequences of intron1 and intron2. Then two exon2-specific primers (IIQ1BU/IIQ1BD) were designed for the species and were used to investigate the B gene diversity of a wild population (Huangshan Mt., n=32) using PCR, cloning and sequencing. In total, 34 distinct alleles were obtained and 2 to 5 alleles were found per individual. The proportion of variable sites for nucleotide and amino acid sequences across the 34 alleles was 16.17% (33/204) and 26.87% (18/67), respectively, and the majority of variable amino acids were located in antigen binding sites (ABS). Based on cDNA data and individual allelic diversity, we conclude that O. tormota possesses at least three class II B loci. These results showed that though the species exhibits a restricted distribution, the Chinese concave-eared frog displays high diversity at the B loci compared to that of other species in Ranidae. Patterns of nucleotide substitution exhibited the signature of positive selection. For example, in the ABS, dN was significantly greater than dS (P <0.05). This pattern was also echoed by results of a likelihood ratio test, and five amino acid sites under significant positive selection were detected by Bayesian analyses. Finally, topology of a Bayesian phylogenetic tree showed that alleles from different anuran families clustered into unique monophyletic groups, but that alleles from different genera within Ranidae did not form monophyletic groups. For example, an allele of Rana clamitans shared a common lineage with alleles of O. tormota. These results suggested that trans-species evolution may be a mechanism that maintains allelic polymorphism of the MHC II B gene across genera in the family Ranidae.

    Application for identification of small mammals by DNA barcoding in Haidong area, Qinghai Province, China
    Ying Ma, Hailong Li, Liang Lu, Qiyong Liu
    Biodiv Sci. 2012, 20 (2):  193-198.  doi:10.3724/SP.J.1003.2012.06188
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    Because of the shortcomings of morphological classification, we studied the feasibility of DNA barcoding in the identification of small mammals. Small mammals belonging to 3 orders, 6 families and 14 genera were collected from the Haidong region in Qinghai Province. We analyzed COI gene sequences from 110 small mammal samples and the results showed that the average intraspecific genetic distance was small than 3%, average interspecific distance ranged from 5% to 10% and intergenus distance 12-19%. The average interspecific genetic distance was significantly greater than the intraspecific genetic distance. A Neighbor-Joining tree showed that samples of the same species formed monophyletic groups with high support value. The NJ tree implied that 6 individuals were misidentified in the field. Our results suggest that the DNA barcoding can increase identification accuracy relative to using morphology alone, and also that the mitochondrial COI gene is an efficacious candidate for DNA barcoding.

    Genetic variability and relationship of 10 Bactrian camel populations revealed by microsatellite markers
    Xiaohong He, Xiuli Han, Weijun Guan, Kechuan Tian, Wenbin Zhang, Yuehui Ma
    Biodiv Sci. 2012, 20 (2):  199-206.  doi:10.3724/SP.J.1003.2012.08159
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    In order to investigate the genetic diversity, genetic relationship, genetic differentiation and possible inbreeding at the molecular level, nine Chinese indigenous Bactrian camel populations and one Mongolian population were sampled and genotyped using 18 microsatellite markers. We did so to provide scientific evidence and technical support for the development of sound policy for the conservation and sustainable utilization of Bactrian camel genetic resources. The results showed that all ten of the Bactrian camel populations had rich genetic diversity with a total of 242 alleles at the 18 loci. The mean number of alleles per locus was 13.44, the average number of effective alleles was 4.18, the mean observed heterozygosity (HO) was 0.5528, and polymorphic information content (PIC) averaged 0.5996. Overall genetic differentiation among the ten populations was highly significant (P < 0.001) with 9.6% of the total genetic variance present among the populations and remaining 90.4% among individuals within the populations. Cluster analysis, principal component analysis and structure analysis all indicated that the ten Bactrian camel populations were separated into two clades: the first included four populations from Xinjiang while the second was made up of the remaining six populations. The genetic differentiation and structuring among the 10 Bactrian camel populations were generally in agreement with the geographic distribution and natural geographic barriers among populations.

    Fish community diversity during spring and autumn in the Yellow Sea off the coast of Shandong
    Zhenbo Lü, Fan Li, Bingqing Xu, Bo Wang
    Biodiv Sci. 2012, 20 (2):  207-214.  doi:10.3724/SP.J.1003.2012.08239
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    Based on trawl survey data from May and October of 2006 in Yellow Sea off the coast of Shandong, China (35º00′-38º00′N, 120º30′-124º00′E), fish composition, dominant species, fish community diversity and size spectra were studied. A total of 61 species were collected, all of them were Osteichthyes species, belonging to 57 genera, 37 families and 13 orders. The most species-rich orders were Perciformes (27 species), Clupeiformes (8 species) and Scorpaendiformes (7 species). There were 7 fish groups according to an analysis of feeding habit: planktivores, planktivores/benthivores, benthivores, benthivores/piscivores, piscivores, omnivores, detritivores. Planktivores accounted for 82.5% of the total catch. There were 3 dominant species (Ammodytes personatus, Engraulis japonicus and Pholis fangi) in spring and 5 dominant species (Engraulis japonicus, Sardinella zunasi, Ammodytes personatus, Larimichthys polyactis and Thryssa kammalensis) in autumn according to analysis of Hill’s diversity; most of these were small-sized species. The highest diversity was found in the coastal waters (particularly in Qingdao and southern of Rushan waters), fish diversity decreased with increasing of water depth, and no significant differences were found between spring and autumn diversity indices. Biomass was negatively correlated with overall diversity and functional group diversity. The slope of size spectra was less than -0.2 both in spring and autumn, and the intercepts were both bigger than 10. When comparing 2006 data to 1985 and 2000 data, slope decreased, and intercept increased. These results might be attributed to the increased dominance of small-sized species in the total catch. Compared with historical data, fish resources in Yellow Sea off the coast of Shandong are obviously declining, with community diversity decreasing and proportion of small-sized individual increasing.

    Soil macro-fauna community diversity and its response to seasonal freeze-thaw in the subalpine/alpine forests of western Sichuan
    Bo Tan, Fuzhong Wu, Wanqin Yang, Lei Xia, , Ao Wang
    Biodiv Sci. 2012, 20 (2):  215-223.  doi:10.3724/SP.J.1003.2012.09138
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    In order to understand the effects of seasonal freeze-thaw on the structure of soil macro-faunal community, we conducted a field experiment in three representative fir (Abies faxoniana) forests at different elevations in the subalpine/alpine forests of western Sichuan. The composition, abundance, and diversity of soil macro-faunal community were investigated in winter (including onset of soil freezing period, soil frozen period, and soil thawing period) and growing season of vegetation from November 2008 to October 2009. A total of 10,763 individuals were collected and, according to preliminary identification, they belonged to 91 families. There were obvious differences in soil macro-faunal community structure between winter and growing season. The dominant groups in winter consisted of Hesperinidae and Sciaridae, while the ordinary groups consisted of Tipulidae, Scydmaenidae and Ceratopogonidae. However, the dominant groups in growing season consisted of Formicidae, Staphylinidae, Hesperinidae and Spirostreptida, and the ordinary groups consisted of Lithobiomorpha, Projapygidae and Muscidae. Moreover, individual density, number of taxonomic groups, and Shannon-Wiener index of soil macro-faunal community tended to decrease and then increase to a distinct peak in the soil thawing period as seasonal freeze-thaw proceeded in winter. In addition, saprozoic species dominated the functional groups in winter, and the proportion of predatory and phytophagous soil macro-faunal species increased in late soil thawing (April 25) and early growing season (May 25). Our results suggest that seasonal freeze-thaw and freezing events significantly influence the structure of soil faunal community, and that changes in the soil faunal community during the transitional period between late soil thawing and the early growing season may have important influences on ecological processes.

    Genetic diversity of Armillaria gallica isolates from China and Europe revealed with ISSR analysis
    Lifu Sun, Kequan Pei, Yanhua Zhang, Jun Zhao, Guoting Yang, Guofu Qin, Yushuang Song, Ruiqing Song
    Biodiv Sci. 2012, 20 (2):  224-230.  doi:10.3724/SP.J.1003.2012.07214
    Abstract ( 3208 )   HTML ( 3 )   PDF (346KB) ( 2579 )   Supplementary Material   Save
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    Armillaria gallica is a cosmopolitan fungal species found in the northern hemisphere, and genetic diversity and similarity between different continental isolates of the species can reveal important large-scale biogeographical patterns. A total of 79 isolates of A. gallica were collected from Europe and China. We estimated the genetic diversity of these isolates using ISSR (inter-simple sequence repeat) markers. Six ISSR primers were employed to identify a total of 210 scorable fragments, of which 202 (96.2%) were polymorphic loci (frequecy<0.95). The average number of polymorphic loci detected with each primer was 33.6. The results indicated that ISSR markers can reflect abundant polymorphism in Armillaria. According to UPGMA clustering analysis, 49 out of 53 Chinese A. gallica isolates clustered into a China Group at the 0.773 similarity level. The genetic divergence of European isolates was significantly higher than predicted; these isolates were clustered into Europe Group A and Group B at the 0.775 and 0.763 similarity level, respectively. The similarity coefficient between the two European groups was only 0.738, but it was 0.770 between China Group and Europe Group A. Some isolates from China and Europe had experienced obvious genetic divergence, and several isolates had lower intraspecific similarity coefficients than interspecific similarity coefficient found in other Armillaria biological species. Our results indicated that considerable genetic differentiation existed between European and Chinese isolates due to geographic isolation, and that these isolates were in the process of allopatric speciation. The differentiation among isolates of A. gallica from Europe was more evident, and Europe is possibly the place of origin for isolates of the species.

    Species composition of alien invasive plants in Heilongjiang Province
    Baojiang Zheng, Lei Pan
    Biodiv Sci. 2012, 20 (2):  231-234.  doi:10.3724/SP.J.1003.2012.04154
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    The number of alien invasive plant species in Heilongjiang Province has increased in recent years due to frequent economic and cultural exchanges with the outside world. To understand the current status of invasive plants, we carried out field surveys for invasive plant species between June 2008 and October 2010. Integrating field and literature data, we compiled a checklist of 41 species of alien invasive plants from 35 genera and 17 families found in this region. Of them, 39 species (95.1%) are herbs. Compositae contains the largest number of species, i.e.12 species (29.3%). Further analysis showed that 22 species (53.7%) have a geographical origin in the Americas, and 14 species (34.2%) in Europe. In relation to introduction pathways, 40 species (97.6%) were intentionally or unintentionally introduced. Floristic analysis of the genera showed that the temperate element, containing 17 genera (68.0%), dominated among nine areal-types. Finally, we discuss the management, monitoring and control of these invasive species and suggest that a specific risk assessment system should be used in Heilongjiang Province.


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