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Table of Content
    Volume 24 Issue 12
    20 December 2016

    All the papers published in Biodiversity Science are freely available on the Internet. The figure shows the word cloud for the keywords of all the open-access papers in Biodiversity Science. Font size reflects the word’s frequency: the word “biodiversity” appeared 122 times, followed by “species diversity” (89 times), “diversity” (65 times), “genetic diversity” (50 times), “conservation” (47 times), etc. The word cloud shows the hotspots and trends that the journal focuses on, including studies at the species and gene levels. To further promote biodiversity data sharing, five data papers are included in this issue. (Data and Figure prepared by Jianping Chen from Shanghai Chenshan Botanical Garden)

    Full Text
    All Papers in This Issue
    Biodiv Sci. 2016, 24 (12):  0-0. 
    Abstract ( 1016 )   PDF (12137KB) ( 5900 )   Save
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    Sharing biodiversity data through academic publishing
    Yuehong Yan, Xiaolei Huang, Keping Ma
    Biodiv Sci. 2016, 24 (12):  1315-1316.  doi:10.17520/biods.2016368
    Abstract ( 1394 )   HTML ( 23 )   PDF (625KB) ( 2499 )   Save
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    Data Paper
    Analysis of publication trends of biodiversity data papers
    Junjie Li, Xiaolei Huang
    Biodiv Sci. 2016, 24 (12):  1317-1324.  doi:10.17520/biods.2016325
    Abstract ( 2300 )   HTML ( 39 )   PDF (733KB) ( 3066 )   Save
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    In recent years, there have been more and more appeals for sharing of biodiversity data. ‘Biodiversity data paper’ has been proposed as a reward mechanism for sharing data by individual scientists. Some data journals dedicated to publishing data papers have been founded. In this paper, we analyze the number of articles, coverage of biological groups, article views, and citations of two representative data journals (Biodiversity Data Journal and Scientific Data). Results show that the number of articles in both data journals has been steadily increasing. Biodiversity data papers cover a wide range of biological groups in Animalia, Plantae and Fungi. The article views and citations also show encouraging performance. These results indicate that data papers are being accepted by more and more researchers. Analysis of author regions of biodiversity data papers indicates a disequilibrium in the data sharing culture among different geographical regions. We suggest Chinese researchers and journals in related fields pay more attention to biodiversity data papers and trends of data sharing policies, as well as improving data sharing practices.

    Data Papers
    De novo transcriptome analysis of the rare fern Monachosorum maximowiczii (Dennstaedtiaceae) endemic to East Asia
    Li Liu, Jiangping Shu, Hongjin Wei, Rui Zhang, Hui Shen, Yuehong Yan
    Biodiv Sci. 2016, 24 (12):  1325-1334.  doi:10.17520/biods.2016231
    Abstract ( 2620 )   HTML ( 65 )   PDF (54880KB) ( 3337 )   Save
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    Monachosorum maximowiczii, which belongs to the family Dennstaedtiaceae, is a unique fern rarely distributed in the middle-high altitudinal areas in East Asia. In order to identify the molecular basis of this species at the transcriptome level, a second generation sequencing technology (RNA-seq) was employed here for the first time. Using Illumina Hiseq 2500 platform, a total of 4.95 Gb raw data were obtained. After filtration, 4.83 Gb clean reads were kept and 101,448 unigene were generated using de novo assembly. Among them, 54,106 unigene were predicted to have a complete open reading frame. The functional annotation of the unigene obtained here was carried out using the Phytozome v11.0 databases. The gene function pattern and participated pathway were further explored based on GO, COG and KEGG annotation. Meanwhile, transcription factors prediction and analysis will provide preliminary insights into mechanisms of Monachosorum maximowiczii for environmental adaptation.

    Datasets of vigilance behavior for three rare ungulates
    Zhongqiu Li
    Biodiv Sci. 2016, 24 (12):  1335-1340.  doi:10.17520/biods.2016284
    Abstract ( 1541 )   HTML ( 23 )   PDF (562KB) ( 2285 )   Save
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    Vigilance is an important strategy of anti-predation. After foraging and reproductive behavior, vigilance behavior has become another important research domain in behavioral ecology. However, original raw data of such kinds of study are seldom shared, despite the mounting studies on vigilance behavior of hundreds of birds and mammals. Here I publish vigilance datasets of three rare ungulates in China collected by focal sampling. These datasets include 716 samples, of which 175 are from Przewalski’s gazelle Procapra przewalskii, 180 are from the Tibetan gazelle P. picticaudata and 361 are from Père David’s deer Elaphurus davidianus. I also include environmental variables, including sex, group type, group size, predation risk and human disturbance. A positive group size effect was found in all three ungulates, and this interacted with sex and predation risk/human disturbance. I attempt to establish a criterion for behavioral data collection, and to improve data sharing and exploration in ethology.

    Diversity and faunal composition of Tenebrionidae from Alxa Plateau
    Long Jia, Guodong Ren, Jianying Zhang
    Biodiv Sci. 2016, 24 (12):  1341-1344.  doi:10.17520/biods.2016106
    Abstract ( 1329 )   HTML ( 15 )   PDF (1434KB) ( 3257 )   Save
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    Data Paper
    Principles behind designing herbarium specimen labels and the R package ‘herblabel’
    Jinlong Zhang, Huiling Zhu, Jingang Liu, Gunter A. Fischer
    Biodiv Sci. 2016, 24 (12):  1345-1352.  doi:10.17520/biods.2016230
    Abstract ( 2806 )   HTML ( 35 )   PDF (1974KB) ( 2939 )   Save
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    Voucher specimens are essential for plant taxonomy, ecology, and plant molecular biology. Collection and identification information should be clearly, accurately and formally printed on herbarium labels, without confusion or spelling mistakes. During the preparation of the labels, data entry should be straight-forward and easy to manage. Ideally, the herbarium label printing software should conduct a thorough evaluation to avoid potential errors, and should issue warnings accordingly. By taking these principles into account, we developed the herblabel R package for generating herbarium labels based on Darwin Core and CVH5.0 data exchange standards. During the implementation of herblabel, the spelling and status of scientific names and the family-genera relationship are compared with the embedded databases to determine potential mistakes or incongruence against APG or other new classification systems. As the template is based on Darwin Core exchange standards, the database could not only be used to generate summaries and reports but also could be shared via GBIF or virtual herbaria. This package will increase efficiency and reduce workload for herbarium specimen preparation, management, and data entry, and should play an important role in cataloging plant diversity.

    Original Papers: Plant Diversity
    Ten-years period of grass and small woody plant dynamics in a 5-ha evergreen forest plot in Baishanzu, Zhejiang Province
    Yunxia Huang, Xuan Xu, Lixiang Zhang, Yue Song, Zhengrong Luo
    Biodiv Sci. 2016, 24 (12):  1353-1363.  doi:10.17520/biods.2016095
    Abstract ( 1270 )   HTML ( 14 )   PDF (4942KB) ( 2907 )   English Version Save
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    Forest dynamics are directly driven by multiple factors, including changes in understory grasses and small woody plants. Yet the dynamics of these small woody plants and grasses as well as underlying ecological forces are still not fully understood, particularly in evergreen forests. Here, we analyzed ten year (from 2003 to 2013) shifts in species importance values, diversity, habitat associations, and distributions of understory small woody plants and grasses (including herbs, herbal lianas and woody plants with diameter at breast height (DBH) < 1 cm) in a 5-ha subtropical forest plot in Baishanzu, Zhejiang, China. Results showed that the number of individuals decreased by 28.7% overall, 76.9% in herbal lianas, and 14.4% in seedlings or saplings of tree species. Species richness of shrubs and grasses decreased notably, while evenness decreased in small woody plant communities and increased in herb communities. Except for Lithocarpus brevicaudatus, Symplocos phyllocalyx, Stauntonia conspicua, Rubus fujianensis, whose importance values increased conversely, correlations between changes of importance values during the ten-years period and initial importance values were positive among erective shrub species and negative among species of other life forms. Shifts in species-habitat associations were complex, as the number of species with significant habitat-associations decreased during the ten year period, except for the increasing richness of species with positive gully associations. Only species diversity in steep slope habitats did not decrease significantly. These findings suggest the small woody plants and grasses of the Baishanzu evergreen forest have not yet reached climax status, and were developing to the climax over 2003 to 2013. Internal community-level processes, such as intraspecific and interspecific competitions, should be dominant factors that drive the forest dynamics.

    Pollination ecotypes and herkogamy variation of Hiptage benghalensis (Malpighiaceae) with mirror-image flowers
    Zhenna Qian, Qianwan Meng, Mingxun Ren
    Biodiv Sci. 2016, 24 (12):  1364-1372.  doi:10.17520/biods.2016248
    Abstract ( 1734 )   HTML ( 12 )   PDF (1290KB) ( 2652 )   English Version Save
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    Herkogamy, the spatial separation of sexual organs within flowers, has long been thought to be a floral adaptation of reducing self pollination in hermaphrodites. Herkogamy of mirror-image flowers in the Asian endemic Hiptage benghalensis (Malpighiaceae) varies greatly between populations on Hainan Island (smaller than 4 mm) and Guizhou Province (larger than 10 mm). Such divergence in herkogamy could be adaptive to pollinator body size, which relates to pollen placement and stigma contact position. Recipient selection between local pollinators and plants may facilitate pollinator assembly in isolated populations, even forming pollination ecotypes. Pollinators were investigated in six geographic populations of H. benghalensis to study whether variations in herkogamy correspond to pollinator size. Molecular markers with nuclear ITS 1/4, chloroplast ycf1b and rbcL were also used to detect genetic differentiation between populations with large or small herkogamy. Our data showed small herkogamy in two populations from Hainan Island and one population from Xishuangbanna (southern Yunnan Province) as they were pollinated by small bees including Apis dorsata and Apis mellifera, with an abdomen width varying from 2 to 4 mm. Two populations from Guizhou Province and one population from Southeast Yunnan with larger herkogamy were pollinated by carpenter bees Xylocopa nasalis and bumble bees (Bombus sp.), with an obvious larger body size with a mean abdomen width of 11 mm. The style length (F = 12.5, P < 0.05) was also significantly different between large versus small herkogamous populations. Genetic data based on nuclear (ITS 1/4) and chloroplast (rbcL and ycf1) DNA also supported the differentiation between small and large herkogamous populations. These results indicated associations between flower and pollinator size, suggesting pollination ecotypes in H. benghalensis. This study indicated that the pollination ecotype in mirror-image flowers was associated with variations in herkogamy.

    Effect of Cry1Ab/c protein residues from Bt cotton-producing areas in regions with marginal water in three provinces in eastern China
    Hua Liu, Xiaolei Chang, Wei Jiang, Lan Bai, Shufeng Zheng, Jinbin Wang, Wei Wang, Aihu Pan, Rongtan Wang, Xueming Tang
    Biodiv Sci. 2016, 24 (12):  1373-1380.  doi:10.17520/biods.2016142
    Abstract ( 1288 )   HTML ( 4 )   PDF (8534KB) ( 1924 )   Save
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    To investigate Cry1Ab/c protein residues in marginal water regions of transgenic cotton-producing areas, this study focused on 15 sampling points from three provinces of eastern China using random sampling. We sampled three consecutive years during the flowering and harvesting of cotton, respectively, purified Cry1Ab/c proteins in these samples were detected using the ELISA (enzyme-linked immunosorbent assay) method. Results showed that: (1) The highest concentration of Cry1Ab/c protein in marginal water reached 0.4 ppb at one sampling point. At the other four monitoring points, the residual concentration of Cry1Ab/c protein was less than 0.04 ppb. (2) The closer the cotton field, the higher the positive detection rate, and the positive rate was 13.3% in the cotton field canals. (3) The positive protein detection rate was 12.4% in planting fields that had been planted for more than 7 years. We also found that during the harvest season the positive protein detection rate was easier to detect than during the flowering period. Our findings indicated that the Bt cotton-producing areas should be properly monitored during the harvest season, in order to reduce the potential impacts of Cry1Ab/c protein on the marginal water sources in transgenic cotton producing areas.

    Effects of rhizosphere soil microorganisms and soil nutrients on competitiveness of Bidens pilosa with different native plants
    Jing Yan, Xiaoya Zhang, Xue Chen, Yue Wang, Fengjuan Zhang, Fanghao Wan
    Biodiv Sci. 2016, 24 (12):  1381-1389.  doi:10.17520/biods.2015365
    Abstract ( 1543 )   HTML ( 11 )   PDF (394KB) ( 2414 )   English Version Save
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    The invasive plant Bidens pilosa has caused losses to agriculture and livestock. We studied the effects of B. pilosa on rhizosphere soil microorganisms and soil nutrients of different native species. The soil microbial species were examined using phospholipid fatty acid (PLFA), and the concentrations of soil nutrients and the activities of soil enzyme activities were measured. Correlation analysis of soil microbial, soil nutrients, and soil enzyme activities was used in Canoco 4.5. Results showed that B. pilosa had a strong ability to aggregate soil microorganisms such as gram-positive bacterium (G+), gram-negative bacterium (G-), and arbuscular mycorrhizal fungi (AMF). The microbial species in the rhizosphere soil of B. pilosa was closely related to the native plant species. Bidens pilosa significantly increased the concentration of organic carbon, while decreasing the concentration of ammonium. The concentrations of available potassium, available phosphorus, and nitrate were strongly related to the native plant species. Correlation analysis showed that 16:00 and 16:1ω5c had a significant influence on the concentration of ammonium. The concentrations of 16:00 and 16:1 ω5c in the rhizosphere soil of B. pilosa were significantly higher than that in the soil of the control, which may lead to the decrease of the concentration of ammonium in the rhizosphere soil of B. pilosa. The concentrations of 15:1 anteiso A and 18:1 ω5c were significantly positively correlated with the concentration of available potassium, and its content were significantly greater than the other treatments in Setaria viridis. The concentration of available potassium in the competition treatment between B. pilosa and S. viridis was significantly higher than the other treatments. The above results show that the invasive plant B. pilosa affected soil enzyme activities and soil nutrients via altering microbial communities, and these changes impacted the native plant species.

    Original Papers: Animal Diversity
    Potential effects of future climate change on suitable habitat of Muntiacus crinifrons, an endangered and endemic species in China
    Juncheng Lei, Sha Wang, Junwei Wang, Jun Wu
    Biodiv Sci. 2016, 24 (12):  1390-1399.  doi:10.17520/biods.2016152
    Abstract ( 1531 )   HTML ( 11 )   PDF (661KB) ( 2476 )   English Version Save
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    Understanding the possible changes of suitable habitats for wild animals in the context of climate change has important implications for creating relevant conservation policies in the future. Based on presence records of black muntjac (Muntiacus crinifrons), which were recorded from 1960s to current day, and nine species distribution models, we simulated black muntjac’s suitable habitat under the future climate scenarios. Future climate scenarios were derived from two greenhouse gas concentrations scenarios (RCP2.6 and RCP8.5), and two future time slices (2050s and 2080s). Results show that, by the 2050s and 2080s, under the scenario of RCP2.6, areas of the suitable habitat of black muntjac will decrease by 11.9% and 6.2%, respectively, while under the scenario of RCP8.5, they will decrease by 36.9% and 52.0%, respectively. Under the scenario of RCP2.6, the areas of ‘core’ landscape for the suitable habitat of black muntjac will decrease by 20.5% and 10.5%, while under the scenario of RCP8.5, they will decrease by 55.2% and 65.2%, respectively. Under the scenario of RCP2.6, the proportion of stable suitable habitat to the suitable habitat under baseline climate conditions are 75.1% and 84.2%, while under the scenario of RCP8.5, they are 48.3% and 35.8%, respectively. In general, using the scenario with RCP2.6, the effects of future climate change on suitable habitat of black muntjac are minimal. In contrast, under the scenario of RCP8.5, the future climate will have drastic effects on suitable habitat for black muntjac. In particular, the area of suitable habitat and its ‘core’ landscape will significantly decrease, and so will the proportion of stable suitable habitat to the suitable habitat under baseline climate conditions. Therefore, we propose to conserve suitable habitat for black muntjac in the border area of Zhejiang, Anhui, and Jiangxi provinces, and to build corridors to connect different nature reserves for black muntjac.

    Research Bulletin
    Habitat features and principal economic characteristics of Eulaliopsis binata germplasm resources
    Fei Liu, Dongsheng Zou, Yelan Yu, Zhanqiang Zhu, Shaoping Wu, Yufeng Zhu
    Biodiv Sci. 2016, 24 (12):  1400-1407.  doi:10.17520/biods.2016244
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    Eulaliopsis binata, a typical wild living resource, is an excellent grass species which is used as material for papermaking and can prevent water loss and soil erosion. Since there are few studies examining the resource collection and assessment of E. binata, in this paper we attempt to use field studies on concentrated areas of Chinese E. binata germplasm resources in 20 counties in nine provinces, collect 20 kinds of E. binata germplasm resources, analyse the principal living environmental characteristics of collection areas of E. binata germplasm resources, and compare the principal economic characteristics of E. binata germplasm resources. Results showed that the collections of E. binata were mainly located in the ranges of 22°-34° N , 101°-114° E, with an elevation of 100-1,000 m, annual average temperatures of 14-22℃, annual sunshine hour ranges of 1,112-2,624 h, and annual average rainfall amounts between 642-2,330 mm. Principal component analysis of climate factors of E. binata showed that the distribution of E. binata was more influenced by temperature and rainfall, while less so by elevation and sunshine hours. The principal economic characteristics of E. binata germplasm resources, such as leaf length, thickness of cell walls, diameter of the cavity, ratio of cell wall and diameter of cavity and yield, show significant differences. Using ward clustering analysis of the principal economic characteristics, the collected E. binata germplasm resources can be divided into 3 categories, of which nine E. binata germplasm resources can be used as reference species for excellent E. binata selection and breeding. The study provides evidence for the selection of improved varieties and utilization of E. binata germplasm resources.

    Diversity and migration routes of raptors in Sichuan Province
    Minyi Liang, Jianghong Ran, Siqi Liang, Yongjie Wu, Xiang Yu
    Biodiv Sci. 2016, 24 (12):  1408-1413.  doi:10.17520/biods.2016238
    Abstract ( 3640 )   HTML ( 26 )   PDF (708KB) ( 3110 )   Save
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    Based on published literatures, museum records, and field investigation records, we collected 2,410 records of raptor distribution data, to study the diversity patterns and migration routes of raptors in Sichuan Province. There were 56 species of raptors (76 species and subspecies) recorded in Sichuan. Forty-one species are from 3 families of Falconiformes, accounting for 64.06% of nationwide Falconiformes species, and fifteen species are from 2 families of Strigiformes, accounting for 48.39% of nationwide Strigiformes species. Five key species of raptors are first-class national protected animals. Raptors have a heterogeneous horizontal distribution pattern in Sichuan, as generally the raptors are richer in the western areas than the eastern areas. The county with the greatest species richness (up to 32) was Pingwu County. Species richness peaked at 1,000-3,500 m on an elevational gradient. Nineteen species of raptors have migratory habits in Sichuan while Jintang County has the greatest number of migration raptors. There are three main migration flyways of raptors in Sichuan. The first one belongs to the Central Asia Migration Flyway passing through the Shiqu and Dege County in the north-west region of Sichuan Province. The second flyway passes through the mountains on western side of the Sichuan Basin from Minshan, Qionglai and Liangshan mountains to Yunnan Province even to Burma. The third flyway passes from the Minshan Mountains to Jintang County and Nanchong Plain and finally reaches Chongqing and Guizhou Province. The latter two flyways belong to the East Asia-Australian Migration Flyway. This study provides a valuable reference for studying and protecting raptors as well as improves our understanding regarding the migration routes of raptors in Sichuan.

    An inventory of county-level biodiversity in Northwest Yunnan
    Jianyong Wu, Hua Peng, Xuelong Jiang, Dayuan Xue, Fan Du, Lianxian Han, Zhuliang Yang, Yumin Shui, Peigui Liu, Xiaojun Yang, Wanggao Jiang, Yuehua Wang, Fuwei Zhao, Rong Dai
    Biodiv Sci. 2016, 24 (12):  1414-1420.  doi:10.17520/biods.2016154
    Abstract ( 2002 )   HTML ( 49 )   PDF (5148KB) ( 3316 )   Save
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    China is one of the world’s richest countries in terms of biodiversity, which has been seriously threatened. In 2010, to effectively protect biodiversity, the State Council of China authorized the Protection Strategy and Action Plan of China Biological Diversity (Year 2010-2030), in which 32 terrestrial Biodiversity Priority Areas were delineated as preferential areas, and background surveys of biodiversity in these areas were also discussed. To protect biodiversity, the Ministry of Environmental Protection of the People’s Republic of China, alongside various research institutions such as Chinese Academy of Sciences and universities, conducted biodiversity background surveys at the county level in 18 counties in Northwest Yunnan of the southern section of the Hengduan Mountains Area from 2010 to 2011. The survey included ecosystems and species. At the ecosystem level, the survey investigated the diversity of vegetation formations within each county. At the species level, the survey investigated diversity of species composition, quantity, and usage of higher plants, vertebrates, and macro-fungi, analyzed the quantities of endemic, rare, and endangered species. The survey culminated in a species inventory at the county level. Based on the survey results, a comparative analysis of biodiversity composition among different counties was conducted. Among the 18 investigated counties, Yulong County, Jianchuan County, Gucheng District, Shangri-La County, and Eryuan County have relatively abundant ecosystem types. While all of these counties have more than 48 formations, Yulong County has the largest number of formations (108 formations). The formations of other counties ranged from 20 to 40. Yulong County not only has the richest vegetation formations, it also has the most abundant number of species (including 4,550 higher plants, 625 vertebrates, and 222 macro-fungi). The region also has a high proportion of endemic species. With respect to higher plants, the ratio of endemic species in most of the counties is about 20%, however, the ratio can approach or exceed 50%. With respect to animal species, the ratio of endemic species in most of the counties is about 10%, with the highest ratio in Heqing County, where 46 endemic species account for 17% of the total species. The authors hold that a comprehensive biodiversity survey is a necessary basis and hence suggest that this study be taken as a case for large-scale biodiversity investigations in the future.

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