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Table of Content
    Volume 20 Issue 1
    20 January 2012

    Shangcheng stout salamander (Pachyhynobius shangchengensis) is endemic to Dabie Mountains of China. Hui Wang et al. found that most di-nucleotide repeat microsatellite loci were involved in the microsatellite DNA family, which resulted in low isolation efficiency in this species. In contrast, no microsatellite DNA family members were found in the tetra-nucleotide repeat microsatellite loci. These results suggest that in the process of microsatellite development for Caudata, t

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    Editorial
    Original Papers
    Effects of different nitrogen regimes on competition between Ambrosia artemisiifolia, an invasive species, and two native species, Artemisia annua and Artemisia mongolica
    Jinping Wang, Lijia Dong, Weiguo Sang
    Biodiv Sci. 2012, 20 (1):  3-11.  doi:10.3724/SP.J.1003.2012.09077
    Abstract ( 2909 )   PDF (567KB) ( 2573 )   Save
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    Evidence suggests that increased nitrogen levels heighten exotic species’ invasiveness and reduce the competitive potential of native species. To reveal the impact of nitrogen deposition on competition between invasive and native species, we compared the growth of Ambrosia artemisiifolia, an invasive species, and two native species, Artemisia annua and Artemisia mongolica under three nitrogen regimes through replacement series experiments in a greenhouse at the Chinese Academy of Science’s Beijing Forest Station. Our results showed that heights of the three species significantly increased, but total biomass did not respond to the enhancement of nitrogen levels in monoculture plantings. When planted in mixtures, however, the heights and total biomass of some species responded to increasing nitrogen levels; Ambrosia artemisiifolia significantly increased, Artemisia annua exhibited no difference, and Artemisia mongolica first increased and then decreased with the increase of nitrogen levels. The growth response of Ambrosia artemisiifolia led to a competitive advantage over two native species. The dynamics of this competition differed at different nitrogen levels: Ambrosia artemisiifolia was a weaker competitor than native species at low level of nitrogen availability, but was a stronger competitor under high nitrogen level. Moreover, the competitive effects of Ambrosia artemisiifolia on Artemisia annua were stronger than on Artemisia mongolica. Nitrogen addition significantly enhanced the competitive ability of Ambrosia artemisiifolia and altered the competition relationship between these species, tipping the scales in favor of the Ambrosia artemisiifolia. Our study indicated that nitrogen deposition associated with global change may facilitate the invasion of Ambrosia artemisiifolia, and may enhance the vulnerability of native communities to invasion.
    A risk analysis system for alien species in urban green spaces and application to the 2010 Expo, Shanghai
    Ruiting Ju, Bo Li
    Biodiv Sci. 2012, 20 (1):  12-23.  doi:10.3724/SP.J.1003.2012.12139
    Abstract ( 2783 )   PDF (718KB) ( 2189 )   Save
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    Invasive species pose risks to regional economies and public health as well as imposing serious damage to natural ecosystems. Urban ecosystems are more susceptible to biological invasions than other ecosystems because they are subjected to more frequent human disturbances. Green space acts as important channels for the spread of alien species into urban ecosystems. Risk analysis can be an effective tool used for preventing invasion of alien species. Although various risk analysis systems have been developed for agricultural and forest ecosystems or nature reserves, the domestic effort to manage risks associated with invasive species in urban green spaces has been limited in China. Therefore, there is a pressing need for formulating scientifically sound methods and approaches for risk analysis in this emerging field. Here, we presented a risk analysis system including risk identification, assessment and management for biological invasions in urban green spaces. Based on risk identification for alien species, we established a risk assessment index that consisted of 4 different layers, i.e. object, item, factor, index layers. A total of 26 index parameters were proposed to assess the risk level, which originated from the risks involved in introduction, colonization, spread and damage of alien species in urban green spaces. In addition, methods for index quantification, weight setting, modeling and risk grading were presented. Applying this system, we analyzed the risks of alien pest species potentially attached to trees brought from Japan to China to green landscapes for the 2010 Expo in Shanghai. Our results showed that 7 species posed a high risk (4 insects, 2 plant pathogens, and 1 plant nematode), 10 species a moderate risk (3 insects, 4 plant pathogens and 3 plant nematodes), and other 2 species (1 insect and 1 nematode) a low or extremely low risk. Based on this analysis, risk management measures were suggested to help local policy-makers set priorities for the management of these alien pests. Monitoring did not reveal the presense of any invasive pests during or after the Expo, suggesting that the risk analysis system may have provided an effective tool for preventing the introduction of invasive alien species and effectively ensuring the ecological security of the 2010 Expo, Shanghai, China.
    The effect of repeated release of the predatory mite Neoseiulus (Amblyseius) cucumeris on arthropod communities in citrus ecosystems
    Jie Ji, Yanxuan Zhang, Xia Chen, Jianzhen Lin, Li Sun
    Biodiv Sci. 2012, 20 (1):  24-31.  doi:10.3724/SP.J.1003.2012.08092
    Abstract ( 2269 )   PDF (530KB) ( 2434 )   Save
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    In order to study the effect of repeated release of Neoseiulus (Amblyseius) cucumeris on the species composition and diversity of arthropod community in citrus ecosystems, we established bio-control orchards, natural orchards and chemical control orchards in the Mawei and Jin’an experimental field of Fuzhou, China. Our results indicated that the species richness of bio-control orchards was higher than that of natural or chemical control orchards at both sites. Diversity and evenness indices were higher in bio-control orchards than those of other orchards in the Mawei site, and those of chemical control orchards were the lowest. Among the variously managed orchards in Jin’an, evenness and diversity indices were highest in the natural orchards and lowest in chemical orchards. Our study suggests that citrus ecosystem arthropod diversity can be enhanced by releasing N. cucumeris to fight against the citrus pest mites while reducing the spraying of pesticide.
    Nekton species composition and biodiversity in Taiwan Strait
    Puqing Song, Jing Zhang, Longshan Lin, Zhangcheng Xu, Xiaoming Zhu
    Biodiv Sci. 2012, 20 (1):  32-40.  doi:10.3724/SP.J.1003.2012.09142
    Abstract ( 2632 )   PDF (458KB) ( 2169 )   Save
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    Based on four bottom trawl surveys (2006–2007) in the Taiwan Strait, nekton species composition, biomass and density distribution, dominant species, and community characteristics were analyzed. We recorded 373 nektonic species including 273 fish species, 81 crustaceans and 19 cephalopods. The mean biomass density index of the study area was estimated to be 24.91 kg/h with fish species, crustacean species and cephalopod species accounting for 65.6%, 21.1% and 13.3% of the total, respectively. Dominant species included Trichiurus japonicus, Portunus haanii, Parargyrops edita, Harpadon nehereus, Trachurus japonicus and Loligo beka. Shannon-Wiener diversity indices (H') ranged from 1.45 to 3.21, with an average of 2.47 and were higher in autumn and winter than in spring and summer. Compared with historical data, nekton resources are obviously declining, with species richness decreasing especially in the Minnan-Taiwan Bank area. Dominant species also exhibited a preponderance of smaller size and age classes compared to historical data.
    Fish community ecology in rocky reef habitat of Ma’an Archipelago. I. Species composition and diversity
    Zhenhua Wang, Shouyu Zhang, Qingman Chen, Qiang Xu, Kai Wang
    Biodiv Sci. 2012, 20 (1):  41-50.  doi:10.3724/SP.J.1003.2012.10168
    Abstract ( 2746 )   PDF (596KB) ( 2569 )   Save
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    Monthly investigations on fish assemblages were carried out in rocky reef habitat (RRH) in the Ma’an Archipelago using multi-mesh trammel nets in 2009, in order to find out the role of RRH in supporting local fish diversity. Fish taxonomic composition and ecological guild groups were used to examine species composition in detail. Indices such as Margalef’s species richness index, Whilm’s species diversity index, Pielou’s species evenness index as well as Pinkas’s IRI were used to analyze the status of fish diversity in RRH. A total of 87 fishes, belonging to 2 classes, 14 orders, 50 families and 73 genera, were collected. Fifty-one fishes from the family Perciformes (accounting 58.6% of the total species), 49 reef fishes (56.3% of the total species) and 7 stocked fishes (8% of the total species) were captured. Sixty-seven percent of total individuals were juveniles. There were 50 warm water fishes, 36 warm temperature fishes and 1 cold temperature fishes. Nineteen species lived on the reef surface, 46 lived in near-ground waters and 22 pelagic fishes frequently appeared in surface waters. Sebastiscus marmoratus was the most dominant ground fish, Nibea albiflora was the most dominant species in near-ground waters and Thryssa kammalensis dominated the surface waters during summer and autumn. We considered 32 fishes to be local species, 55 were seasonal species and another 11 were casual species. Significant seasonal variation was detected; the lowest and highest diversity levels were found, respectively, in February and September. Our studies suggests that rocky reef habitat in Ma’an Archipelago was mostly used by reef fishes and warm water species. Juvenile fishes congregated in large numbers in these habitats during spring and summer. RRH also serves as habitat for fishes released from stock enhancement programs. We conclude that RRH are important coastal habitats because they offer feeding, spawning and nursing grounds for many fishes, especially juveniles of economically-important species. However, fish diversity has dropped in comparison to its original status in RRH habitats. We suggest that more attention should be paid to the management and conservation of rocky reef habitat.
    Structural characteristics of di-nucleotide/tetra-nucleotide repeat microsatellite DNA in Pachyhynobius shangchengensis genomes and its effect on isolation
    Hui Wang, Baowei Zhang, Wenbo Shi, Xia Luo, Lizhi Zhou, Demin Han, Qing Chang
    Biodiv Sci. 2012, 20 (1):  51-58.  doi:10.3724/SP.J.1003.2012.08168
    Abstract ( 2390 )   PDF (510KB) ( 2180 )   Save
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    A low success ratio is often encountered in the microsatellite isolation from the species of Caudata. In the present study, di-nucleotide/tetra-nucleotide repeat microsatellite loci were isolated following the FLASCO (fast isolation by AFLP of sequences containing repeats) approach and the sequences were analyzed for the purpose of learning how microsatellite structure impacted on isolation efficiency. We found that most di-nucleotide repeat microsatellite loci were involved in the microsatellite DNA family, which resulted in low isolation efficiency. In contrast, no microsatellite DNA family members were found in the tetra-nucleotide repeat microsatellite loci. On the basis of analysis of the three microsatellite DNA families found in the present study, there were significant differences in the extent of variation between the upstream and downstream flanking sequences in same microsatellite DNA family. This variation was the highest in the sequence sections adjacent to the core repeated units, but more conservative in other regions, which might reflect the complexity of the microsatellite DNA family evolution. These results suggest that in the process of microsatellite development for Caudata, we must pay attention to interference from microsatellite DNA family evolution. The choice of appropriate nucleotide repeats is key to obtaining a high isolation efficiency.
    Effects of plant functional groups and plant species on soil microbial composition in a Inner Mongolian grassland
    Ying Chen, Xiaoxiao Li, Jiaoyan Ying, Cunzhu Liang, Yongfei Bai
    Biodiv Sci. 2012, 20 (1):  59-65.  doi:10.3724/SP.J.1003.2012.07160
    Abstract ( 2961 )   PDF (458KB) ( 2952 )   Save
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    In order to study the effect of plant community composition on soil microbial communities in a typical Inner Mongolian grassland, the abundance and community structure of bacteria and fungi in bulk soils under different plant functional groups and in soils from the rhizosphere of different grass species were analyzed using real-time PCR and automated ribosomal intergenic spacer analysis (ARISA) under plant functional group removal treatments. Our results indicated that changes in plant functional group affect bacterial abundance, but not fungal abundance or bacterial/fungal community structure in bulk soil. The abundance of bacteria and fungi in the rhizosphere soil varied with plant species. Cluster analysis revealed that community structure of bacteria and fungi also varied among plant species in the rhizosphere soil but not in the bulk soil. which was more evident for bacteria. Our results point to the ways in which plant species can influence soil microbial and fungal communities through the action of their roots.
    Methodologies
    Criteria and methods for assessing the threat status of ecosystem
    Guoke Chen, Keping Ma
    Biodiv Sci. 2012, 20 (1):  66-75.  doi:10.3724/SP.J.1003.2012.10171
    Abstract ( 2572 )   PDF (376KB) ( 2456 )   Save
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    Assessing the threat status of ecosystems is a useful tool for understanding biodiversity loss on Earth. In 2008, the International Union for Conservation of Nature (IUCN) established a working group at the fourth World Conservation Congress to develop quantitative categories and criteria for assessing ecosystem threat status. These categories and criteria were similar to those used to assess extinction risk for species. This working group strove to establish red lists of ecosystems by applying these criteria to ecosystems at local, regional, and global scales. Ecosystem red lists were designed to be complementary to species red lists for use in creating biodiversity conservation policies. The criteria used for assessment were grouped into four classes: short-term decline in distribution or ecological function, historical declines in distribution or ecological function, small current distribution with decline in distribution or ecological function, or very restricted current distribution. In this paper, we illustrate the use of these criteria for assessing ecosystem threat status; we used literature data on the areas of occupancy for four ecosystems in China’s Liaohe Delta in 1988 and 2006 to evaluate the threat status of these four ecosystems. We also discuss challenges that lie ahead for this method of assessment. Measures of ecosystem distribution and area of occupancy should be based on proper spatial scales. Appropriate quantitative methods are also needed to measure changes in ecosystem function. The final proposed assessment protocol will be presented for further discussion at the 2012 World Conservation Congress.
    Applying cluster analysis and Google Maps in the study of large-scale species occurrence data
    Kunchi Lai, Youhua Cheng, Yuehchih Chen, Yousheng Li, Kwangtsao Shao
    Biodiv Sci. 2012, 20 (1):  76-85.  doi:10.3724/SP.J.1003.2012.10131
    Abstract ( 2928 )   PDF (856KB) ( 2173 )   Save
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    The primary species occurrence data include the data on animal and plant specimens in museums and herbaria, as well as species observations. TaiBIF (Taiwan Biodiversity Information Facility) data portal has integrated 26 datasets so far, resulting in more than 1.5 million species occurrence data; 85% of them are geo-referenced. This study utilizes more than 8,800 Cyprinidae occurrence data from 11 datasets and uses three different types of clustering algorithms—grid-based, partition-based, and density-based—to produce different spatial visualization results. It aims to resolve the problems of efficacy and poor visualization when large scales of species occurrence data are presented in Google Maps. The study also explores the comparative differences between the results obtained from the three clustering algorithms and the expert opinion range maps of Cyprinidae. It hopes to identify a quick and efficient way to present species distribution data, in turn help researchers to extract knowledge from large amount of data so that the knowledge can be tapped as important reference for ecological conservation efforts.
    Short RNAs, potential novel molecular markers for higher plants
    Wen Liu, Hong Liang, Biren Yang, Jiewen Lin, Yanji Hu
    Biodiv Sci. 2012, 20 (1):  86-93.  doi:10.3724/SP.J.1003.2012.08123
    Abstract ( 2623 )   PDF (520KB) ( 2590 )   Save
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    In recent years, molecular biology techniques, especially molecular markers, have been applied to the study of species similarity and evolutionary relationships in the field of plant systematics. Here, we attempted to find a small fragment of RNA that could be used as a molecular marker for the rapid identification of plant taxa above genus. To do so, total nucleic acids were isolated from 53 species of higher plants using SDS extracting solution containing HAc-NaAc buffer. The isolated nucleic acids were subjected to 7% polyacrylamide gel electrophoresis (PAGE). Results showed: (1) A large number of bands, which were at the length of 100–200 bases and with clear shape. The bands patterns were stable and repeatable. These segments were confirmed to be short RNAs by DNaseI and RNaseA treatment; (2) No obvious differences in band patterns were found among different varieties, organs, sexualities and ploidy of kiwifruit seedlings. A similar case existed in mung bean seedlings after different light treatment periods; (3) Banding patterns of plants in the same family were polymorphic, with differences mainly related to geographic isolation. Higher taxonomic categories had a higher percentage of polymorphic band (PPB) and higher values of polymorphism information content (PIC) than lower taxonomic categories; (4) Three to six clear bands with a length of 100–200 bases, whose band patterns were related to the phylogenic relationship, were found through comparison of short RNAs from 53 species of ferns, gymnosperms and angiosperms. Thus, short RNAs with a length of 100–200 bases showed potential as a molecular marker for determining inter- or intrafamily phylogenic relationships.
    Reviews
    Advancements and prospects in forest seed rain studies
    Yanjun Du, Keping Ma
    Biodiv Sci. 2012, 20 (1):  94-107.  doi:10.3724/SP.J.1003.2012.14161
    Abstract ( 2431 )   PDF (482KB) ( 2262 )   Save
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    Seed dispersal links the reproductive cycle of adult plants with the establishment of their offspring and is widely recognized as a process that has a profound effect on the structure of tree communities. Although ecologists as early as Darwin realized the importance of seed dispersal, the scientific study of seed rain did not gain momentum until the early 1980s. A considerable amount of seed rain research has been conducted since then. Here we focused on seed rain studies of woody plants in forests. Seed rain monitoring methods are introduced, including seedtrap set, seed collection, separation, and identification. We also review recent progress in these studies—temporal and spatial variation in seed rain (seasonal, intra-annual, and spatial variations), recruitment limitation and its role in species coexistence, testing the negative density-dependent hypothesis, and comparisons between seed rain and later life history phases (soil seed bank, seedling, sapling and adult). We recommend that future studies should pay attention to conducting long-term seed rain monitoring, examining cross-site recruitment limitation, exploring whether negative density-dependence at the earliest stages of regeneration is greater in the tropics than at higher latitudes, and developing exciting new techniques including the analysis of stable isotope ratios and molecular genetic markers.
    The impact of climate change on birds: a review
    Weiwei Wu, Haigen Xu, Jun Wu, Mingchang Cao
    Biodiv Sci. 2012, 20 (1):  108-115.  doi:10.3724/SP.J.1003.2012.08152
    Abstract ( 2974 )   PDF (349KB) ( 3710 )   Save
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    The impact of climate change on biodiversity has become a hot issue. This paper reviews the effects of climate change on avian distribution, phenology and population dynamics according to the results of the latest research. Due to climate change, bird distributions have shifted towards high-latitude and high-altitude areas, which is changing more quickly than before. However, the breeding area which bird lived was changed different from the non-breedings. In addition, the ranges of many species have decreased, the timing of oviposition and migration have become more variable, and populations of many species have declined. We also summarize the major methods used to forecast the effects of future climate scenarios on birds, and discuss how evolution, biotic interactions and dispersal ability affect the results of predictions. We found that more and more scientists using the integrated models than the single ones nowadays, a new advice using the mechanistic models has been proved well, and evolution has become a big problem for the prediction from the latest researches. The suggestions are as follows: (1) a system of avian protection should be established as soon as possible in China. (2) people should devise and evaluate some models in research work.

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