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Molecular mechanism for transcription and replication of RNA virus
LIU Qing-Zhen, LI Ling-Yun, QI Yi-Peng, YANG Fu-Hua
Biodiv Sci    2001, 09 (3): 294-300.   DOI: 10.17520/biods.2001044
Abstract2750)      PDF(pc) (275KB)(2552)       Save
RNA viruses are much more than DNA viruses in quantity and species in nature. It can be divided into many types of viruses according to genomic type. Recently , many researchers indicate that the ret ron existing in Myxobacteria , which carries only one reverse transcriptase gene , is the possible ancestor for all kinds of viruses , with the following evolution model : Retron →Ret roposon →Ret ransposon →Ret rovirus →Pararet rovirus →DNA viruses. It is very different between transcription/ replication of RNA virus and DNA virus genomes in many aspects. RNA-dependent RNA polymerase is the major catalyst for transcription/ replication. Initiation sites for RNA virus t ranscription/ replication are specific structures [poly (A) or tRNA] at 3′ terminal region. Internal stop results in transcription but reading through to 5′end resulting in replication. RNA viruses use the following four kinds of templates in transcription/ replication : ( + ) ssRNA template , ( - ) ssRNA template , ( + ) aRNA template , ( - ) aRNA template. The mechanism of selective regulation on RNA templates is very complex and the acknowledgements of the regulation mechanism are quite few up to now. Selecting template and the binding of transcription factors with RNA pol to form replicon are two major regulatory means. Besides promoter and transcription factors , 5′UTR and 3′UTR also regulate the transcription of RNA viruses.
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Promoting diversity inventory and monitoring of birds through the camera-trapping network in China: status, challenges and future outlook
Shuyi Zhu, Fei Duan, Sheng Li
Biodiv Sci    2017, 25 (10): 1114-1122.   DOI: 10.17520/biods.2017057
Abstract524)   HTML3)    PDF(pc) (1945KB)(1096)       Save

During the past two decades, camera-trapping has been widely used in biodiversity monitoring and wildlife research across China. Most of the existing camera-trapping projects focus on mammals, and birds are frequently considered in by-catch records. We analyzed 230 wildlife camera-trapping research projects in China since 1992, on the basis of an exhaustive review of Chinese and English literature, including published articles, conference reports, public news, and additional unpublished datasets. Results showed that at least 393 wild bird species, belonging to 17 orders and 56 families and accounting for 28.67% of the total number of bird species in China, have been documented using camera-trapping since 1992. The order with the most recorded species was Passeriformes (268). On the family level, Turdidae had the highest number of recorded species (58), followed by Timaliidae (50) and Phasianidae (42). There were 23 families that each only had one recorded species. Ground- and understory-dwelling forest birds accounted for the majority of all birds recorded, in terms of either species richness or camera detections. Published bird records were characterized by regional imbalances. Sichuan and Yunnan provinces were the most surveyed provinces, with 16 and 14 sites, respectively. The highest species richness was recorded in Sichuan (160), followed by Yunnan (91) and Zhejiang (66). A total of 104 new regionally recorded species were reported. Given the fact that there is still an abundance of camera-trapping data that has not been published, we speculated that the actual recorded bird species should be higher. These results indicated that camera-trapping can produce considerable bird distribution data of high accuracy, high quality and large amounts, which may provide a significant contribution to biodiversity monitoring and regional inventories of birds in China. Terrestrial birds, including Galliformes, Turdidae and Timaliidae, should be included as one of the target groups in current and future monitoring networks using standardized camera-trapping techniques, and such networks could also complement data and support the inventory and diversity monitoring of other taxa.

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Cited: CSCD(2)
From nature reserve to national park system pilot: Changes of environmental coverage in the Three-River-Source National Park and implications for amphibian and reptile conservation
Huijie Qiao,Xiaoyi Wang,Wei Wang,Zhenhua Luo,Ke Tang,Yan Huang,Shengnan Yang,Weiwei Cao,Xinquan Zhao,Jianping Jiang,Junhua Hu
Biodiv Sci    2018, 26 (2): 202-209.   DOI: 10.17520/biods.2017305
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The Three-River-Source (TRS) region, which harbors an evolutionarily unique and impressively large portion of plateau biodiversity, is an important national ecological security shelter zone. Acting as the first system pilot in China, the TRS National Park will be turned into both the exhibition of nature conservation and a heritage area of ecological culture on the Qinghai-Tibetan Plateau. To better contribute to the construction of the TRS National Park, we compared the TRS National Park with the TRS and Kekexili Nature Reserves with respect to elevation, annual mean temperature and annual precipitation. By combining the environmental conditions of the occurrences of four species of amphibians and reptiles (i.e., Rana kukunoris, Nanorana pleskei, Scutiger boulengeri, and Phrynocephalus vlangalii) both inside and outside the national park, we explored potential opportunities and challenges for the conservation of poor-dispersal-ability species (including amphibians and reptiles) during construction of the TRS National Park. While the national park and the nature reserves had large overlap in geographical space, the environmental conditions were different between them. The preferred environmental conditions of the four species were mostly not included in the TRS National Park, but were included in the nature reserves. Given the unique geographical location of the TRS region and its sensitivity to climate change, the effective protection of amphibians and reptiles in this region will not only contribute to maintaining genetic diversity of species and the integrality of regional ecosystems, but also will help to achieve the goal of the TRS National Park and assist with the construction of ecological civilization. Thus, within the TRS National Park, to strengthen basic biological research, it is important to conduct long-term monitoring studies of population dynamics and community structure. Based on this, the potential effects of environmental changes on the distribution, genetic diversity, behavior, morphological traits, population dynamics and community of amphibians and reptiles could be understood, with the aim of achieving their sustainable survival within the TRS National Park in the face of global change.

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Cited: CSCD(2)
Red List of China’s Vertebrates
Zhigang Jiang, Jianping Jiang, Yuezhao Wang, E Zhang, Yanyun Zhang, Lili Li, Feng Xie, Bo Cai, Liang Cao, Guangmei Zheng, Lu Dong, Zhengwang Zhang, Ping Ding, Zhenhua Luo, Changqing Ding, Zhijun Ma, Songhua Tang, Wenxuan Cao, Chunwang Li, Huijian Hu, Yong Ma, Yi Wu, Yingxiang Wang, Kaiya Zhou, Shaoying Liu, Yueying Chen, Jiatang Li, Zuojian Feng, Yan Wang, Bin Wang, Cheng Li, Xuelin Song, Lei Cai, Chunxin Zang, Yan Zeng, Zhibin Meng, Hongxia Fang, Xiaoge Ping
Biodiv Sci    2016, 24 (5): 500-551.   DOI: 10.17520/biods.2016076
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Cited: CSCD(40)
Natural hybridization and speciation
Yuguo Wang
Biodiv Sci    2017, 25 (6): 565-576.   DOI: 10.17520/biods.2017041
Abstract1008)   HTML7)    PDF(pc) (762KB)(1575)       Save

Natural hybridization plays a pivotal role in the formation of new species during the evolution of organisms. There are two principal types of hybrid speciation: polyploidization and homoploid hybrid speciation. The former has been regarded as an important force driving plant speciation, whereas the latter has proved to be a main mode of speciation based on an increasing number of cases, which have reported successful crosses between the species at the same ploidy level. However, only a few cases of homoploid hybrid speciation have been documented when strict criteria are applied. Therefore, molecular evidence involving more genomic loci and morphological investigations from different kinds of hybrid zones, as well as assessments of existing speciation models and new computer stimulations, are required for further understanding the genetic basis of the initial and entire process of speciation. Through the historical reconstruction of gene flow between diverging lineages, additional organismal models for hybrid speciation need to be developed to reveal the effects of natural selection on the formation of reproductive isolation, and to discern the ecologically adaptive changes and the formation rules of novel diversity in the process of hybrid speciation. Here I briefly review the history of studies examining natural hybridization and speciation to introduce concept changes, research methods, and the latest advances of natural hybridization and speciation, to identify the unsolved core and basic scientific questions and to provide feasible suggestions for future studies and the protection of biodiversity involved in natural hybridization.

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Cited: CSCD(6)
All Papers in This Issue
Biodiv Sci   
Threatened Species List of China’s Higher Plants
Haining Qin, Yong Yang, Shiyong Dong, Qiang He, Yu Jia, Lina Zhao, Shengxiang Yu, Huiyuan Liu, Bo Liu, Yuehong Yan, Jianying Xiang, Nianhe Xia, Hua Peng, Zhenyu Li, Zhixiang Zhang, Xingjin He, Linke Yin, Yulin Lin, Quanru Liu, Yuantong Hou, Yan Liu, Qixin Liu, Wei Cao, Jianqiang Li, Shilong Chen, Xiaohua Jin, Tiangang Gao, Wenli Chen, Haiying Ma, Yuying Geng, Xiaofeng Jin, Chaoyang Chang, Hong Jiang, Lei Cai, Chunxin Zang, Jianyong Wu, Jianfei Ye, Yangjun Lai, Bing Liu, Qinwen Lin, Naxin Xue
Biodiv Sci    2017, 25 (7): 696-744.   DOI: 10.17520/biods.2017144
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Cited: CSCD(6)
Some scientific questions for ecosystem services
GUO Zhong-Wei, GAN Ya-Ling
Biodiv Sci    2003, 11 (1): 63-69.   DOI: 10.17520/biods.2003009
Abstract2726)      PDF(pc) (237KB)(3401)       Save
Ecosystem services and the natural capital stocks that produce them are critical to the functioning of the Earth′s life supporting system. They contribute to human welfare, both directly and indirectly, and therefore represent part of the total economic value of the planet. Four scientific quastions about the functions of ecosystem services are discussed in this paper. They are: 1) study of the integration, amount and spatial location of functions of ecosystem services; 2) the spatial transfer of functions of ecosystem services; 3) the relationship between ecosystem service and ecological security; and 4) the sustainable use of ecosystem services. The heterogeneity in the structure of ecosystem's results in heterogeneity of their functions. Consequentially, there is spatial heterogeneity in the functions of ecosystem services. Thus, it is necessary to analyze the functions of ecosystem services by qualitative, quantitative and spatial means. Some functions of ecosystem services can be transferred spatially by various methods, and produce benefits at areas far removed from their habitats and range of suitable conditions. This phenomenon is called spatial transfer of ecosystem services. Thus, characteristic ecosystem services can bring economic values to a region of larger area than that covered by the ecosystem′s habitats. Ecosystem services provide supporting system for humans, and their strengths depend on ecological capital stock. Ecological capital stock illustrates the capability of sustainable development of a country. Ecological capital stock of an ecosystem relies in turn on the function and the structure of the ecosystem. Endangerment of ecosystem service raises a question for ecological security. In many regions ecological resources are rare. To use ecological resources sustainably, local communities should be urged to develop their economies by means of managing ecosystem services, i.e., to industrialize the management of ecosystem services. These four scientific questions for ecosystem services are related to each other. The aim of discussing them is to focus study on ecosystem services in the future.
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Cited: CSCD(38)
China’s mammal diversity (2nd edition)
Zhigang Jiang, Shaoying Liu, Yi Wu, Xuelong Jiang, Kaiya Zhou
Biodiv Sci    2017, 25 (8): 886-895.   DOI: 10.17520/biods.2017098
Abstract1100)   HTML25)    PDF(pc) (823KB)(2251)       Save

Due to recent modifications of mammalian taxonomy, discoveries of mammalogy in China, and conservation needs of the country, China’s mammal diversity inventory is in urgent need of an update. We collected new species and records of mammal species in China from the literature since March 2015, adopted the new taxonomy, incorporated our own research, and added mammalian species of the Zangnan Region, to renew the inventory of mammal diversity in the country. The major changes in the new version of the inventory are the elevation of the order Cetartiodactyla to the super order Cetartiodactyla and the split of the order Cetartiodactyla in Jiang et al (2015) into orders Cetacea and Artiodactyla, respectively. Chodsigoa hoffmanni C. furva and Mesechinus sp. were added to the order Eulipotyphla. In the order Chiroptera, Murina fanjingshanensis, Myotis rufoniger and Rhinolophus subbadius were added, while Myotis hirsutus and Miniopterus fuscus were deleted from the inventory. In the order Primates, Hoolock tianxing, Trachypithecus pileatus, Nycticebus coucang and Hoolock hoolock were added to the inventory. In the order Carnivora, Melursus ursinus, Canis aureus, Vulpes bengakensis, Herpestes edwardsii, and Felis viverrinus were added. We reclassified the species in the order Artiodactyla according to the taxonomy of the Handbook of the Mammals of the World, Vol. 2, Ungulates. Ovis ammon, O. collium, Budorcas taxicolor, and Muntiacus muntjak were added to the order. All sika deer in the country were grouped as a single species, Cervus nippon, and all moose were grouped as a single species, Alces alces. Cervus alashanicus and C. macneilli as well as the dwarf blue sheep, Psuodois sharferi, were deleted, and the species of the Tragulus in Xishuangbanna was listed as Tragulus sp. In the order Cetacea, Platanista gangetica was added while Delphinus capensis was deleted. In the order Rodentia, new species, Typhlomys nanus, Neodon medogensis and N. nyalamensis, Bandicota bengalensis as well as Myospalax cansus, Biswamoyopterus biswasi, Niviventer niviventer, Mus booduga; and one species, Typhlomys daloushanensis, which was elevated from the status of subspecies, were added to the inventory, however, Hadromys humei was deleted from the inventory. The taxonomy of Arvicolini of Cricetidae was renewed. Caprolagus hispidus and Lepus nigricollis were added to the order Lagomorpha and the taxonomy of Ochotona was renewed, with 5 species downgraded from the status of species to subspecies while 4 were elevated from subspecies to species. Altogether there are 29 pika species in China. However, O. princeps, O. collaris, O. hoffinanni, O. rufescens and O. pusilla are not found in the country. The new inventory of China’s mammals has 13 orders, 56 families, 248 genera and 693 species. Compared with that reported by Jiang et al (2015), there is now an additional order, family, three genera and 20 species in the new mammalian diversity inventory. Of the mammalian species in country, the statuses of 18 species, mostly rodents, are still in dispute amongst mammalogists. There are 146 endemic mammalian species in China, which accounted for 21% of the total mammal species in the country. Of those endemic species by order, the highest endemic rate is found in Lagomorpha (37%), followed by Eulipotyphla (35%) and Artiodactyla (25%). Overall, China has the richest mammal diversity in the world.

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Cited: CSCD(3)
Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses
Jian-Feng Mao, Yongpeng Ma, Renchao Zhou
Biodiv Sci    2017, 25 (6): 577-599.   DOI: 10.17520/biods.2017097
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Hybridization among diverging (interspecific or intraspecific) groups involves gene flow and genetic recombination. Increasingly, studies have shown that hybridization, a process of genetic exchanges, occurs widely in the divergence and unity of animals, plants, and microorganisms, and acts as an important mechanism for the formation and maintenance of biological diversity. The rapid development of high-throughput sequencing technology and the widespread application of genome-level techniques provides an unprecedented opportunity for us to further evaluate the universality and evolutionary significance of hybridization. However, selecting appropriate research techniques and strategies to detect the potential hybridization and evaluate its characteristics becomes a common question. In this review, we attempt to synthesize methods from phylogenetics and population genetics of the genomic era to provide biodiversity and evolutionary researchers a practical reference for testing hybridization.

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Cited: CSCD(1)
Progress and prospect of climate change and marine biodiversity
Jianguo Du, William W.L. Cheung, Bin Chen, Qiulin Zhou, Shengyun Yang, Guanqiong Ye
Biodiv Sci    2012, 20 (6): 745-754.   DOI: 10.3724/SP.J.1003.2012.10051
Abstract3477)      PDF(pc) (280KB)(3772)       Save
The relationship between biodiversity and climate change is a primary focal point of the Convention on Biological Diversity. Marine biodiversity is an important part of global biodiversity, therefore, it is imperative to have a thorough understanding of the relationship of climate change and marine organism. We reviewed the research about the relationship of climate changes and marine target species like Clupea pallasi, marine population structure such as zooplankton in East China Sea, marine ecosystems like coral reef and mangrove, and forecasting models such as dynamics bioclimate envelope models. We also identified the current status of climate change in China. Based on our analysis, we developed a set of research strategies including attaching importance to target species, enhancing marine animal population, identifying sensitive marine ecosystems, continuing long term studies, developing simulations on marine biodiversity under different climate change scenarios, and using ocean geographyic information system (GIS).
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Cited: CSCD(6)
China’s mammalian diversity
Zhigang Jiang,Yong Ma,Yi Wu,Yingxiang Wang,Zuojian Feng,Kaiya Zhou,Shaoying Liu,Zhenhua Luo,Chunwang Li
Biodiv Sci    2015, 23 (3): 351-364.   DOI: 10.17520/biods.2014202
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China’s mammalian fauna is unique: it possesses the endemic species and genera of the Qinghai-Tibetan Plateau; it has the relic families, Ailuropodidae and Lipotidae, of the Tertiary Period; more than half of the species of the Ochotonidae in the country are endemic; furthermore China is also the country with world most abundant ungulate diversity. In the new millennia, changes to the taxonomy of mammals of world were proposed. New mammalian species and new mammals were reported in China. Thus it is necessary to renew the inventory of China’s mammal diversity. During the compiling of The Red List of Endangered Species in China: Mammals, we collected the available data on China’s mammals (including those of Taiwan) and formed The Checklist of China’s Mammal Species 2015. For taxonomy of orders, we followed the existing theory using molecular phylogeny whereas for the classification of families and the taxa below family level, we followed the A Complete Checklist of Mammal Species and Subspecies in China: A Taxonomic and Geographic Reference by Wang (2003) and Mammal Species of the World: A Taxonomic and Geographic Reference by Wilson & Reeder (2005). We also adopted Ungulate Taxonomy by Groves & Grubb (2011) to classify the ungulates in China. The initial list included species recorded in taxonomic books and field guides, new species and new records in literature before March 31, 2015. After five evaluation meetings and two rounds of evaluation by correspondence, we finalized The Checklist of China’s Mammal Species 2015, which includes 12 orders, 55 families, 245 genera and 673 species. Among those species, 18 new species (including 11 discovered with molecular biology methods, the validity of the species are still in dispute among zoologists), 18 new species records in country, and 60 subspecies were elevated to the status of species were added to the checklist. According to literature and expertise, we deleted 52 species which are not found in China. Of them, specimens of some species were collected only once, and then never been found again during following surveys. Taxonomists hold different opinions on 20 Glires, and those species need further investigation. Compared with the data of IUCN Red List (2014), the number of mammal species in China recorded in the study is surpassed that of Indonisia (670), China became the country with the most abundant mammal species in the world. The mammals in China accounted for 12.3% of the world total numbers of mammalian species. There are 150 endemic mammals in China, which accounted for 22.3% of the national total. 43% of the species in Lagomorpha are endemics to the country. The endemic ratio of Ochotonidae is even higher, 52% of the total. Endemic ratio of Eulipotyphla is 35%. About one fifth of Primates, Chiroptera and Rodentia in China are also endemics, including 12 new bat species discovered in the country during recent decade. The Checklist of China’s Mammal Species 2015 provides the most updated baseline information for biodiversity research and conservation.

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Cited: CSCD(3)
Families and genera of Chinese angiosperms: a synoptic classification based on APG III
Bing Liu,Jianfei Ye,Su Liu,Yuan Wang,Yong Yang,Yangjun Lai,Gang Zeng,Qinwen Lin
Biodiv Sci    2015, 23 (2): 225-231.   DOI: 10.17520/biods.2015052
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Angiosperms constitute the most diverse lineage of higher plants and are represented by ca. 300,000 living species that dominate the vegetation of terrestrial ecosystems. Number and composition of families, genera, and species are important to understanding global and regional biodiversity. Due to the rapid development of molecular systematics, circumscriptions of many traditional angiosperm families and genera have been revised. This study investigates circumscriptions of families and genera of native and introduced angiosperms in China according to the APG III classification system and recent phylogenetic studies. Results showed that there are 258 native and 55 introduced families (including 6 naturalized families), and 2,872 native and 1,605 introduced genera (including 152 naturalized genera) in China. A brief introduction to the historical and recent changes of circumscriptions of families and genera occurring in China was also provided. Our list included 115 newly recorded families and 1,729 newly recorded genera when compared to Flora Reipublicae Popularis Sinicae, and 85 newly recorded families and 1,531newly recorded genera when compared to Flora of China.

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Cited: CSCD(7)
Community assembly: the relative importance of neutral theory and niche theory
Kechang Niu, Yining Liu, Zehao Shen, Fangliang He, Jingyun Fang
Biodiv Sci    2009, 17 (6): 579-593.   DOI: 10.3724/SP.J.1003.2009.09142
Abstract7201)      PDF(pc) (439KB)(9961)       Save
Understanding species coexistence and the maintenance of biodiversity has long been the central interest of ecologists. The niche-based theory of community assembly has dominated community ecology for nearly a century, yet understanding of the mechanisms of species coexistence has remained elusive. The newly developed neutral theory of biodiversity has offered a promising alternative to the niche paradigm. The analytical elegance and simplicity of the neutral theory and its predictive power have made the theory widely popular. However, it is the very same simplicity of the theory (e.g. the symmetric assumption) that makes the theory vulnerable to stark criticisms. Widespread empirical evidence has shown that species in communities are not functionally symmetric; ecological equivalence is more a conceptual simplicity than a biological real-ism. Recognizing that niche and neutral processes do not have to diametrically oppose each other and a community is likely determined by the interplay of the two processes, ecologists currently are searching to reconcile the two theories by either incorporating drift into niche theory or niche into the neutral framework. However, this reconciliation process is still at its very early stage, we expect this direction will lead to a more complete understanding of community assembly mechanisms. In this paper, we provide a review on the brief histories of the niche and neutral theories, with the focus on comparing the distinct importance of the two theories in explaining community assembly. We discuss in details several integrated models that attempt to unify the niche and neutral theories. We argue that it is an essential step for any successful theory to with-stand substantial experimental and field tests. The experimental tests of neutral theories are an important di-rection that has currently not received due attention.
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Cited: CSCD(73)
Marine biodiversity under global climate change
Jun Sun,Mao Lin,Meng-Hsien Chen,Kuidong Xu
Biodiv Sci    2016, 24 (7): 737-738.   DOI: 10.17520/biods.2016195
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Cited: CSCD(1)
Beta-diversity partitioning: methods, applications and perspectives
Xingfeng Si, Yuhao Zhao, Chuanwu Chen, Peng Ren, Di Zeng, Lingbing Wu, Ping Ding
Biodiv Sci    2017, 25 (5): 464-480.   DOI: 10.17520/biods.2017024
Abstract2491)   HTML30)    PDF(pc) (1371KB)(2505)       Save

Beta diversity describes the variation in species composition among communities within a region and it is determined by two antithetic processes: species turnover (or species replacement), and nestedness (or difference in richness). Beta-diversity partitioning aims to separate these two processes when examining species composition among communities, and to reveal their underlying mechanisms. Since 2010, the partitioning methods were proposed following two dominant frameworks: the BAS method proposed by Andrés Baselga in 2010 (partitioning overall beta diversity into turnover and nestedness components) and the POD method proposed by János Podani and Dénes Schmera in 2011 and José C. Carvalho et al. in 2012 (partitioning overall beta diversity into species replacement and richness difference components). With the continuous debate on the nature of the BAS and POD methods, studies on beta-diversity partitioning have developed rapidly worldwide. We reviewed journal articles in the field of beta-diversity partitioning since 2010. Results showed that the number of publications and citations using the BAS method were greater than those using the POD method (75% vs. 20%). In those publications, most of study sites were located in Europe (45%) and research taxa were dominated by animals (64%). Here, we introduce the history and development of beta-diversity partitioning, potential applications in studying biodiversity distributions across spatial-temporal scales (latitudinal/altitudinal gradients, habitat fragmentation, seasonal and annual dynamics), multiple-faceted diversity (taxonomic, functional and phylogenetic diversity), and comparisons among various biological taxa. We point out the following directions in the field of beta-diversity partitioning in the future: (1) the synthesis and comparative analysis of the methods of beta-diversity partitioning; (2) examining patterns of overall beta diversity and its components by incorporating species abundance; and (3) testing the generality of results yielded from beta-diversity partitioning across large scales.

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Structural features of root-associated fungus-plant interaction networks in the tropical montane rain forest of Jianfengling, China
Yang Siqi,Zhang Qi,Song Xiqiang,Wang Jian,Li Yide,Xu Han,Guo Shouyu,Ding Qiong
Biodiv Sci    2019, 27 (3): 314-326.   DOI: 10.17520/biods.2018339
Accepted: 09 April 2019

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Functionally diverse root-associated fungi may differentially interact with host plants, potentially affecting the assembly processes of belowground plant and fungi communities. Here, we applied the Illumina Miseq sequencing technique to identify root-associated fungi of plants which were co-dominant in a tropical montane rain forest on Hainan Island, China. Structural features of bipartite networks were compared among the whole root-associated, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungus-plant interactions. A total of 297,831 fungal ITS1 sequences were obtained from eight families including Aceraceae, Annonaceae, Apocynaceae, Aquifoliaceae, Arecaceae, Fagaceae, Lauraceae, and Oleaceae. Fungal sequences were assigned to 1,279 OTUs comprised of Ascomycota (748 OTUs), Basidiomycota (354), Glomeromycota (80), and unidentified fungi (97). At least three functional groups of fungi i.e. putatively ECM (40 OTUs, represented 23.4% of the total fungal reads), AM (40, 13.9%) and saprophyte (83, 19.8%) were prevalent in the core root-associated fungal community (420 OTUs) of the tropical montane rain forest. Network analysis indicated that AM, ECM and root-associated fungus-plant interaction network showed structural features which cannot be predicate by null models assuming species interact randomly. Community level indices behaved differently among different ecotypes of fungus-plant interactions. Specifically, the degree of nestedness (NODF) and connectance were higher, while specialization was lower in the AM interaction network than the expected values from null models. In contrast, the ECM interaction network had a significantly higher degree of specialization and lower nestedness and connectance than the null models. At guild levels, plant niche overlap of AM and ECM interactions are higher and lower than the null model, respectively. Niche breadth of ECM fungi was narrower than that of AM fungi. Co-occurrence patterns of plant and fungus further confirmed competition for resources was intense in ECM interaction network (high C-score of both plants and fungi) and weak in the AM interaction network (low C-score). These findings suggest that at least two modes of interspecific interactions are critical for the assembly and coexistence of root-associated fungal communities, i.e. redundancy (nestedness) of AM interactions, and niche differentiation (specialization) of ECM interactions. Here we provide a comprehensive exploration of the interactions among functionally diverse root-associated fungal guild within a forest, which is key to understand the mechanisms maintaining species coexistence in tropical forests.

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Advancing phylogeography with chloroplast DNA markers
Hu Ying, Wang Xi, Zhang Xinxin, Zhou Wei, Chen Xiaoyang, Hu Xinsheng
Biodiv Sci    2019, 27 (2): 219-234.   DOI: 10.17520/biods.2018319
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Phylogeography seeks to identify the historical ecological and evolutionary processes underlying modern-day phylogenetic relationships across a spatial gradient. Owing to the characteristics of uniparental inheritance, low mutation rates and haploid, chloroplast DNA (cpDNA) markers record the events occurring in historical long-term evolutionary processes to different extents, and hence aid in understanding the mechanisms for phylogeographic variation. Here we discuss how these characteristics affect cpDNA marker selection, how they increase or reduce population genetic differentiation, how they lengthen or shorten the average gene coalescent times, how they promote or impede gene introgression among species and how the process of lineage sorting functions from polyphyly to paraphyly to monophyly. We reviewed the theoretical bases of these mechanisms, as well as the progress made in empirical studies regarding the theories of phylogeographic variation. Because of the heterogeneity of DNA sites in mutation rate, selection strength and interactions with genetic drift effects, one study to examine the genome-wide pattern of phylogeography will be necessary in the future. This must include the analysis of differential gene introgression and gene flow among sites, as well as the distribution of the differential phases of lineage sorting along the chloroplast genome.

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China’s key protected species lists, their criteria and management
Jiang Zhigang
Biodiv Sci    2019, 27 (6): 698-703.   DOI: 10.17520/biods.2019089
Accepted: 08 July 2019

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China’s key protected species lists include the List of State Key Protected Wild Animals (LSKPWA), the List of Terrestrial Wildlife with Important Ecological, Scientific and Social Values, and the lists of local key protected wild animals. After the amendment and implementation of the Wild Animal Protection Law of the People’s Republic of China in 2017, the revision of the LSKPWA is on the agenda. In order to revise the list of the state key protected species, the relationship between these lists should be delineated to reflect the priority of protection and to facilitate administration and to divide the responsibility of protection between the central and local governments. It is recommended to determine the level of key protected wildlife species according to their attributes of endangerment, endemism, rareness, preciousness and management requirement. By adopting the Principle of Clump Listing, related species or the higher taxa such as a whole genus even a whole family should be included in the lists of protected species as far as possible. It is also practical to list a subspecies or a population as a management unit on the species protection list. In addition, to reflect the new provisions of the amended Wild Animal Protection Law of the People’s Republic of China, it is necessary to distinguish domesticated and wild populations, those populations which have been artificially successfully bred with mature technology and stable production traits should be exempted from the listing. Thus, using the Principle of Splitting Listing to solve the real problems in conservation. In addition, taxonomic changes should be closely tracked and species list should be updated in time. It is also necessary to formulate criteria for protection levels, to develop guidelines for species recovery plan after their listing and to design amendment procedure for the list. It is important to formulate populations and habitats recovery plan for each key protected species. Through periodic evaluation of the listed species, the listed species are upgraded, downgraded, deleted or maintain its status for the needs of dynamic management of rare and endangered wild animals.

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Camera-trapping survey on the diversity of mammals and birds in Qianjiangyuan National Park, Zhejiang Province
Jianping Yu Jiangyue Wang Huiyun Xiao Xiaonan Chen Shengwen Chen Sheng Li Xiaoli Shen
Biodiv Sci    2019, 27 (12): 0-0.   DOI: 10.17520/biods.2019345
Accepted: 09 February 2020

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From May 2014 to April 2019, we conducted camera-trapping surveys in the Qianjiangyuan National Park, Zhejiang Province. We divided the park into 267 1 km × 1 km grids, with 3 fixed survey stations (>300 m apart from each other) in each grid. One trip camera was set in each grid and rotated among the stations within this grid every four months. In the Gutianshan section of the park, the cameras have been running for 14 rotations from 2014-2019. The survey started in Hetian, Qixi and Changhong in 2018 and the cameras have been rotated once in Qixi and twice in Hetian and Changhong. With a survey effort of 140,413 camera-days from 741 stations in 253 grids, we obtained 268,833 pictures/videos resulting in 74,368 independent detections. The survey recorded 21 wild mammal and 72 bird species, as well as 5 domestic animal species. Among the species, 2 (Black Muntjac Muntiacus crinifrons and Elliot's Pheasant Syrmaticus ellioti) are Class-I and 17 are Class-II national protected animals, accounting for 20.4% of total recorded species. Four species are listed by IUCN Red List as Vulnerable and five as Near Threatened, accounting for 9.7% of the total recorded species. One species is listed as Endangered, nine as Vulnerable and ten as Near Threatened by China’s Red List of threatened vertebrates, accounting for 21.5% of the total recorded species. The most detected mammal species is Reeve’s Muntjac Muntiacus reevesi, and the most detected bird species is Silver Pheasant Lophura nycthemera. Our results provide reliable baseline information on the species composition, their spatial distribution and relative abundance of mammals and birds in the Qianjiangyuan National Park.
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The spatial pattern of species richness and diversity centers of gymno-sperm in China
Guo Li, Zehao Shen, Tsunshen Ying, Jingyun Fang
Biodiv Sci    2009, 17 (3): 272-279.   DOI: 10.3724/SP.J.1003.2009.08327
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China has the richest flora of gymnosperm in the world, which is crucial for understanding the change of global distribution and phylogeny of gymnosperm. We mapped the geographical range of 202 native gymnosperm species in China with records of altitudinal range and horizontal distribution at the county level, and explored the spatial distribution characteristics of Chinese gymnosperm at the family, genus and species levels. The uniqueness and similarity among the richness centers were analyzed with respect to their gymnosperm family and genus composition, and the endemism. Generally, Chinese gymnosperm shows a decreasing trend of richness from south to north. The richness is high in mountainous areas and low in large plains and on large plateaus. From the species, genus to family levels, the area with high gymnosperm rich-ness increases, and the center with high richness shifts southward. About 85% of all Chinese gymnosperm species are harbored in just 5% of Chinese land area. We classified these regions into six richness centers: (1) Eastern Himalaya-Hengduan Mountains-Qinling Mountains; (2) joint area of Yunnan-Guizhou-Guangxi and the South Mountain Ranges; (3) central China mountains; (4) Huangshan-Wuyi Mountains; (5) southern mountains of Hainan Island; and (6) central part of Changbai Mountains. The floristic relationship of gym-nosperm among the centers is obviously related with their geographic location, and the effect of isolation by distance. Among the six centers, Hengduan Mountains is a major variation center of gymnosperm in China.
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Cited: CSCD(20)
Genetic diversity in seven Chinese indigenous sheep breeds based on microsatellite analysis
YANG Yan, MA Yue-Hui, LU Shen-Jin, ZHANG Ying-Han
Biodiv Sci    2004, 12 (6): 586-593.   DOI: 10.17520/biods.2004074
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Genetic diversity in seven Chinese indigenous sheep breeds was estimated using 26 microsatellite markers. The allele frequency, mean heterozygosity, polymorphism information content, effective number of alleles, genetic distance,and dendrogram analysis were used to assess the genetic variability and genetic relationships among the seven breeds. A total of 278 alleles were detected, and the 26 loci were highly polymorphic. The effective number of alleles ranged from 2.1288 to 13.3924, mean heterozygosity of loci from 0.0629 to 0.5903, mean heterozygosity of breeds from 0.3633 to 0.4489, and polymorphism information content from 0.6628 to 0.8712. In the Neighbor-Joining tree based on Nei′s standard genetic distance, the seven sheep breeds formed two groups: Hazake sheep, Altay Fat-rumped sheep and Bayinbuluke sheep were closely related, then clustered with Baizang sheep and Heizang sheep; and the second group consisted of Hu sheep and Jinzhong sheep. The dendrogram relationship between different sheep breeds was generally in accordance with their origins, breeding history and localities.
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How did nucleus and sexual reproduction come into being?
Ping Xie
Biodiv Sci    2016, 24 (8): 966-976.   DOI: 10.17520/biods.2016057
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The origin of eukaryote is a fundamental, forbidding evolutionary puzzle, and the popular scenarios of eukaryogenesis are far from being clear. So far, there have been various theories (e.g., syntrophic model, autogenous model, viral eukaryogenesis model, exomembrane hypothesis), but few explain why. I observed that C-value (the amount of DNA contained within a haploid nucleus) increased by 3.5 orders of magnitude from prokaryote to eukaryotes, which is inconceivably close to the packing ratio of DNA in extant eukaryotes. Thus, it is never convincing to explain eukaryogenesis solely by using accident phagocytosis, symbiosis or parasitism (the influential endosymbiont theory unfortunately took the wrong turning!), but what is important is to explain why genome increased so sharply. This may be mainly related to DNA replication errors or polyploidization, of course not completely ruling out the possible contribution from lateral gene flow or genetic integration between individuals of different species. It is above suspicion that successful packing of DNA (finally into chromosome) was a key step towards eukaryogenesis, of course also accompanied with structural differentiation in cell and development of more subtle and complex cell division, and so on. This paper presents “packing and structurization hypothesis” to explain eukaryogenesis. In addition, from a molecular genetic point of view, sexual reproduction is never a mystery as it is just a process to merge two individual genomes, by which diverse genetic information of the species are dispersed into its individuals. On the other hand, from an ecological point of view, the original motivation of “sex” was accidently coupled with dormancy.

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Biodiversity and ecosystem multifunctionality: advances and perspectives
Wei Xu,Zhiyuan Ma,Xin Jing,Jin-Sheng He
Biodiv Sci    2016, 24 (1): 55-.   DOI: 10.17520/biods.2015091
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As global biodiversity losses accelerate, there is increasing evidence shows that there may be negative impacts on ecosystem functioning, such as declines in plant primary productivity and imbalances in nutrient cycling. Thus, it is critical to understand the relationship between biodiversity and ecosystem functioning (BEF). However, ecosystems can provide multiple functions simultaneously (ecosystem multifunctionality, EMF). Since 2007, the quantification of relationships between biodiversity and ecosystem multifunctionality (BEMF) has generated additional questions and controversies, such as the lack of consensus in appropriate multifunctionality indices and uncertain trade-offs among ecosystem functions. In this review, we briefly summarize the history of BEMF studies and the methods of EMF quantification, then outline the mechanisms of EMF maintenance and current research progress. We emphasize the importance of optimizing EMF quantifications and investigating the relationship between different dimensions of biodiversity and EMF. We also provide suggestions and directions for future research on BEMF.

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Cited: CSCD(8)
Plant functional traits, functional diversity, and ecosystem functioning: current knowledge and perspectives
Lingjie Lei,Deliang Kong,Xiaoming Li,Zhenxing Zhou,Guoyong Li
Biodiv Sci    2016, 24 (8): 922-931.   DOI: 10.17520/biods.2015295
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Increasing attention has recently been focused on the linkages between plant functional traits and ecosystem functioning. A comprehensive understanding of these linkages can facilitate to address the ecological consequences of plant species loss induced by human activities and climate change, and provide theoretical support for ecological restoration and ecosystem management. In recent twenty years, the evidence of strong correlations between plant functional traits and changes in ecosystem processes is growing. More importantly, ecosystem functioning can be predicted more precisely, using plant functional trait diversity (i.e., functional diversity) than species diversity. In this paper, we first defined plant functional traits and their important roles in determining ecosystem processes. Then, we review recent advances in the relationships between ecosystem functions and plant functional traits and their diversity. Finally, we propose several important future research directions, including (1) exploration of the relationships between aboveground and belowground plant traits and their roles in determining ecosystem functioning, (2) incorporation of the impacts of consumer and global environmental change into the correlation between plant functional traits and ecosystem functioning, (3) effects of functional diversity on ecosystem multifunctionality, and (4) examination of the functional diversity-ecosystem functioning relationship at different temporal and spatial scales.

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Cited: CSCD(7)
Phylogeography of East Asia’s Tertiary relict plants: current progress and future prospects
Yingxiong Qiu,Qixiang Lu,Yonghua Zhang,Yanan Cao
Biodiv Sci    2017, 25 (2): 136-146.   DOI: 10.17520/biods.2016292
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In this review, based on recent studies of population genetics and phylogeographics of East Asia’s Tertiary relict plants, we have outlined the main phylogeographic patterns and processes. We also summarize common geographic and environmental factors which may contribute to the phylogeographic patterns of East Asia’s Tertiary relict plants and present future challenges and research prospects. There are four recurrent phylogeographic scenarios identified by different case studies, including: (1) the global cooling and aridification during the Middle and Late Miocene induced recent speciation, with climate change during the Late Pliocene and Pleistocene accounting for their intra-specific lineage divergence, genetic diversification and demographic expansion/contraction. The latitudinal contraction/expansion can lead to the formation of “suture zone” for some relict plants; (2) the effects of the formation of the glacial East China Sea land bridge, as a “corridor” or “filter”, have to account not only for habitat preferences per se but also for other biological features of different relict plant species; (3) the uplift of the Qinghai-Tibet Plateau (QTP) during the Late Pliocene and the intensification of East Asian monsoon system (EAMS) are the most suggestive factors responsible for the major phylogeographic break between the western and eastern lineages across the Sichuan Basin and northwestern arid regions; and (4) some Tertiary relict plants migrated southward to Taiwan from mainland China or Japan before the Pleistocene under global climatic cooling and aridification since the Late Miocene, and refugial isolation that occurred between Taiwan and mainland Asia accelerated vicariant lineage diversification and speciation. Overall, both historical and contemporary geography and environment have affected the distribution, genetic diversity, lineage divergence and speciation of East Asia’s Tertiary relict plants. Finally, we emphasize notable gaps in our knowledge due to the long-term application of simple molecular clock based on very limited genetic markers, and outline future research prospects for disentangling the evolution and biogeographic history of East Asia’s Tertiary relict flora. We present the utilization of genome data and biogeography models and integrative phylogeographic research of multi-taxon communities as possible future directions.

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Cited: CSCD(1)
All Papers in This Issue
Biodiv Sci    2019, 27 (11): 0-0.  
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Hot topics for Biodiversity Science
Keping Ma
Biodiv Sci    2016, 24 (1): 1-2.   DOI: 10.17520/biods.2016029
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Cited: CSCD(11)
A rapid approach for assessing the conservation effectiveness of the most concerned endangered species in China
Lei Gu,Cheng Wen,Mei Luo,Hao Wang,Zhi Lü
Biodiv Sci    2015, 23 (5): 583-590.   DOI: 10.17520/biods.2015115
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By establishing a set of grading standards, conservation effectiveness was assessed rapidly for 174 of the most concerned endangered species in China, including all the Category I National Protected plant and animal species, and avian species defined as CR and EN by the IUCN Red List. Based on the data from published research articles, satellite remote sensing, field surveys and information collected by citizen scientists, the assessment was obtained by grading population dynamics, information perfections, potential habitat changes and protected area coverage of simulated distributions. Results show that the overall conservation status deteriorated during 2000-2013. The average grades of all four indexes were negative. The conservation status of 26 species improved, while 32 species maintained their status and 116 species worsened. We also investigated the trends of 9,338 published research articles in reference to 746 threatened species during 2000-2013. The numbers of studied species and research articles increased every year, but less than 1/3 of the total threatened species had been studied in any single year. Research concentrated on the star species and the species with economic value, for example, the giant panda (Ailuropoda melanoleuca) contributed to 11.33% of all research articles. On the other hand, scientific research and basic information were lacking in most other threatened species.

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Cited: CSCD(4)
On the system of national parks and the path of development in China
Xiaoping Tang
Biodiv Sci    2014, 22 (4): 427-430.   DOI: 10.3724/SP.J.1003.2014.14113
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Cited: CSCD(4)
Potential distribution range and conservation strategies for the endangered species Amygdalus pedunculata
Jianmin Chu, Yifu Li, Lei Zhang, Bin Li, Mingyuan Gao, Xiaoqian Tang, Jianwei Ni, Xinqiao Xu
Biodiv Sci    2017, 25 (8): 799-806.   DOI: 10.17520/biods.2015218
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The endangered shrub species Amygdalus pedunculata is distributed in Inner Mongolia Autonomous Region and Shaanxi Province, China. However, little is known about its resource quantity and conservation status. A field investigation was conducted to determine the natural distribution range of A. pedunculata. Eight environmental factors were chosen to build models with the genetic algorithm for rule-set prediction (GARP) model and maximum entropy (MaxEnt) model. We predicted the potential distribution of A. pedunculata in China. Using four model evaluation metrics (Kappa, true skill statistic (TSS), overall accuracy and area under the receiver operating characteristic curve (AUC)), we assessed the predictive performance of both models. The Jackknife method was used to investigate the most important environmental factors for the distribution of A. pedunculata. The results indicated that both models were effective for predicting the distribution of A. pedunculata, but MaxEnt performed better than GARP in terms of the four evaluation metrics. The species was predicted to have a broad suitable area, which ranged from the south of Daxing’anling to the east of Helan Mountains and the Ulan Buh Desert. Amygdalus pedunculata is mainly distributed in the middle regions of Inner Mongolia, including Mu Us Sandy Land, Kubuqi desert, Otindag Sandy Land, and the Wulashan and Daqingshan Mountains. Low suitable sites occurred in some regions of Liaoning, Hebei, Shanxi and Shaanxi. Besides, and there were some sporadic low suitable areas in the middle regions of the Ningxia Hui Autonomous Region and Gansu Province. Variable importance analysis showed that the variables relevant to precipitation had more significant effects on the geographic distribution of A. pedunculata. These results have important implications for resource conservation and ecology including the revegetation of semi-arid ecosystems.

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Simulation of the potential range of Pistacia weinmannifolia in Southwest China with climate change based on the maximum-entropy (Maxent) model
Lingxiao Ying,Ye Liu,Shaotian Chen,Zehao Shen
Biodiv Sci    2016, 24 (4): 453-461.   DOI: 10.17520/biods.2015246
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Pistacia weinmannifolia is a characteristic species of dry valleys in Southwest China. In this study, 165 presence points of P. weinmannifolia were identified through field surveys, along with point data of 22 environmental factors. The suitable habitat model was formulated using the maximum-entropy (Maxent) algorithm and applied to simulate the potential range of the species in Southwest China, and to project the change of species range in past and future climate scenarios. The results indicate that the Maxent model gave a high accuracy in habitat predictions for P. weinmannifolia. Temperature seasonality, minimum temperature and precipitation were the major constraining climatic factors. Contemporarily, the environment suitable for P. weinmannifolia was located in the dry valleys of major rivers in Southwest China, and the regions was characterized by decreased temperature variability, no temperatures below 0°C, and low precipitation. Simulations using climate scenarios of the Last Inter-Glacial (LIG) and Last Glacial Maximum (LGM) periods indicated that the distribution of P. weinmannifolia was centered around the valleys of major rivers in Southwest China, substantially expanded eastward first, and retreated westward following climate change during glacial and inter-glacial periods, supporting the hypothesis of “glacial out-of-Hengduan Mts.”. Under the future climate scenario (2061-2080) with three representative concentration pathways (RCPs), the potential distribution of P. weinmannifolia was projected to migrate eastward to the valleys in the adjacent region of the Yunnan-Guizhou Plateau and Sichuan Basin, and the adjacent region of the Plateau and western Guangxi, reflecting a high possibility of increasing dryness in the river valleys in the future, while its current distribution might disappear. The potential distribution of P. weinmannifolia would decrease by 33% in Southwest China under the future scenario with both RCP2.6 and 4.5, but would increase with RCP8.5.

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Cited: CSCD(9)
Ecological niche modeling and its applications in biodiversity conservation
Gengping Zhu,Guoqing Liu,Wenjun Bu,Yubao Gao
Biodiv Sci    2013, 21 (1): 90-98.   DOI: 10.3724/SP.J.1003.2013.09106
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Based on the environmental variables that associated with species’ occurrence records, ecological niche modeling (ENM) seeks to characterize environmental conditions suitable for a particular species and then identify where suitable environmental habitats are distributed in the space. Recently, ENM has been used increasingly in biological invasion, conservation biology, biological responses to climate change, disease spatial transmission, and variety aspects of ecology and evolutionary biology research. However, the theoretical background of these applications is generally poorly understood, leading to artifactual conclusions in some studies (e.g. niche differentiation during species’ invasion). In this paper we discuss the relationship between niche and geographic distribution and introduce the theoretical basis of ENM, along with relationships between the niche and ENM. Abiotic/biotic, historical and dispersal factors are three key elements that determine species’ geographic distributions at different scales. By using environmental variables derived from distributional records, ENM is based on observations that already include effects of biotic interactions, therefore ENM is used to characterize somewhere between the realized niche and potential niche, not the fundamental niche. Grinnellian and Eltonian niches are both manifested in ENM calibration, depending on the types of variables used to fit model, the natural spatial scale at which they can be measured, and the dispersal of individuals throughout the environment. Applications of ENM in understanding ecological requirements of species, discovery of new species or populations, nature reserve design, predicting potential invasion, modeling biological responses to climate change, niche conservatism, and species delimitation are discussed in this paper.

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Cited: CSCD(49)
Ecological characteristics of mountains and research issues of mountain ecology
FANG Jing-Yun, SHEN Ze-Hao, CUI Hai-Ting
Biodiv Sci    2004, 12 (1): 10-19.   DOI: 10.17520/biods.2004003
Abstract4777)      PDF(pc) (341KB)(4271)       Save
Mountains are complex ecological systems, with unique structures and functions, and have rich biodiversity, water and mineral resources, and opportunities for tourism. Mountain ecology is the study of mountain structures, functions, and processes, as well as the exploration, sustainable utilization and conservation of mountain resources. In this paper, we review the effects of major topographic elements on ecological factors, summarize the ecological benefits of mountains, and discuss the current research issues and topics for Mountain Ecology. It is emphasized that in topography of mountainous areas is the most critical controlling factor for ecological structures, functions, and processes. Topography affects the abundance and distribution of organisms by modifying solar radiation, heat, moisture, soil and fertility. For this reason, topography and topographyinduced ecological phenomena and processes are considered to be the most critical topics in mountain ecology. Topographic research addresses such issues as ecological complexity, biodiversity, mountain climate changes, mountain ecological engineering, mountain sustainable development, and quantification of topographic elements (elevation, slope, aspect, and location). Among these, developing appropriate methods for quantifying topographic elements is a key technique. We also suggest a need for a synthetic study of relationships between humans and the natural world based mountain sustainable development.
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Cited: CSCD(81)
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Biodiv Sci   
Soil microbial diversity observation in China: current situation and future consideration
Xiangzhen Li,Liangdong Guo,Jiabao Li,Minjie Yao
Biodiv Sci    2016, 24 (11): 1240-1248.   DOI: 10.17520/biods.2015345
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Soil microbial diversity has not been extensively observed due to technique limitations. With the development of the high-throughput sequencing technique and bioinformatics, much progress has been made in observations of microbial diversity. Currently, international microbiome initiatives have been founded (including the Earth Microbial Project). However, problems in these projects include a lack of dynamic observations, differences in observational methods, and data integration. The soil microbial observation network (SMON) is an important part of the Chinese Biodiversity Monitoring and Research Network (Sino BON). The observational network initially selected field observation sites in forest ecosystems along a temperature and precipitation gradient from south to north, in grassland ecosystems along a precipitation transect from east to west, and in typical wetland and agricultural ecosystems in China. Field ecological observation stations have been established in these selected ecosystems. Key tasks for the SMON are to observe spatial and temporal dynamics of soil microbial communities and functional genes in various ecosystems, including bacteria, archaea, fungi, and lichens. Observational data will be published periodically in the format of database, annals, and illustrated handbooks. Key methods used in the SMON are high- throughput sequencing, metagenomics, and bioinformatics. A soil biota database is currently being constructed to store observational data for public inquiry and analysis. Through the efforts of SMON, we plan to explore the driving mechanisms of spatial and temporal variations of soil microbial communities and their functional genes, and understand the relationships between microbial diversity and ecosystem function, in order to predict microbial dynamics under global environmental change scenarios, and to design strategies to protect soil microbial diversity and properly utilize microbial resources.

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Effect of the Maxent model’s complexity on the prediction of species potential distributions
Gengping Zhu,Huijie Qiao
Biodiv Sci    2016, 24 (10): 1189-1196.   DOI: 10.17520/biods.2016265
Abstract988)   HTML4)    PDF(pc) (597KB)(1877)       Save

Ecological niche modeling (ENM) is widely used in the study of biological invasions and conservation biology. Maxent is the most popular algorithm and is being increasingly used to estimate species’ realized and potential distributions. Most modelers use the default Maxent setting to fit niche models, which originated from an earlier study containing 266 species, with the purpose of seeking their realized distributions. However, recent studies have shown that Maxent uses a complex machine learning method. It is sensitive to sampling bias and tends to overfit training data, and is only transferrable at low thresholds. Default settings based on Maxent outputs are sometimes not reliable, making it difficult to interpret. Using Halyomorpha halys and classical modeling approaches (i.e., niche models that were calibrated in native East Asia and transferred to North America), we tested the complexity and performance of the Maxent model under different settings of regulation multipliers and feature combinations, and chose a fine-tuned setting with the lowest complexity. We then compared the response curves and model interpolative and extrapolative validations between models calibrated using default and fine-tuned settings. Our purpose was to explore the effects of the model’s complexity on niche model performance in order to improve the development and application of Maxent in China. We argue that selection of environmental variables is crucial for model calibration, which should include ecological relevance and spatial correlation. Reducing sampling bias and delimitating a proper geographic background, together with the comparison of response curves and complexity of Maxent models built under different settings, is very important for fitting a good niche model. In the case of H. halys, the default and fine-tuned settings are different, however the response curve is much smoother in the fine-tuned model, and the omission error is lower in introduced areas when compared to default model, suggesting that the fine-tuned model reflects the response of H. halys to environmental factors more reasonably and precisely predicts the potential distribution.

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Cited: CSCD(6)
A method for assessing species diversity conservation value of nature reserves
Ziliang Guo,Shaohua Xing,Guofa Cui
Biodiv Sci    2017, 25 (3): 312-324.   DOI: 10.17520/biods.2016350
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In order to provide a scientific basis for upgrading the level of a nature reserve (NR) and selecting the appropriate management type, the conservation priority of NRs should be identified. How to objectively identify conservation priorities has become a key problem. We propose a mathematical method to comprehensively assess species diversity conservation values by comparing existing evaluation indexes and methods, consulting experts and processing indexes quantitatively. This evaluation method includes the following indices: the wild plant diversity conservation value index; wild animal diversity conservation value index; rare and endangered wild plant diversity conservation value index; and the rare and endangered wild animal diversity conservation value index of a NR. Meanwhile, 39 NRs in North China Warm Temperate Region and 67 NRs in Northeast China Temperate Region were selected as case studies to verify methods, based on species diversity data of the NRs. The evaluation results revealed that some provincial NRs could be recommended for an upgrade to national NRs, due to high species diversity conservation values, including the Nandagang Wetland and Liaohe River Source NRs of Hebei, Wuling Mountain NR of Beijing in the North China Warm Temperate Region, the Jingpo Lake, Dajia River, and Cuibei Wetland NRs of Heilongjiang in the Northeast China Temperate Region. The computation method showed a great advantage in comparing species (various groups) diversity conservation values for different NRs and determining the conservation priority sequence. Moreover, there were significant differences in the species diversity conservation value of NR among different natural conservation geographical areas, and types of NRs.

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Using NCBIminer to search and download nucleotide sequences from GenBank
Xiaoting Xu,Zhiheng Wang,Dimitar Dimitrov,Carsten Rahbek
Biodiv Sci    2015, 23 (4): 550-555.   DOI: 10.17520/biods.2015120
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GenBank is the leading public genetic resources database and currently contains over 1012 base pairs from about 300,000 formally described species. It offers valuable resources for studies on the evolution of species, genes, and genomes. However, difficulties in GenBank data mining hinder the potential wide application of this tool for big data collection. To address this issue, we introduce new bioinformatics software —NCBIminer. NCBIminer is a freely available, cross-platform, and user-friendly software for mining nucleotide sequences from GenBank. The main purpose of NCBIminer is to download sequences for user required genes and taxonomic groups based on gene names, types, and one or several reference sequences. The program algorithms have been described elsewhere and here, we focus on introducing the details in the usage of the program including how to install, run, and set parameters.

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Frequency dependent fitness in different evolved Escherichia coli lines
Chuan Ni,Biru Zhu,Dayong Zhang
Biodiv Sci    2016, 24 (9): 1056-1061.   DOI: 10.17520/biods.2016143
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Differences in fitness between two species or genotypes is usually assumed to be constant when competition experiments are used to measure relative fitness in evolutionary experiments. However, interactions between competitors may lead to frequency-dependence in fitness. We measured the relative fitness of two types of evolved lines of Escherichia coli under different initial relative frequencies to analyze the effects of initial relative frequency on relative fitness. Competed with the low nitrogen evolved lines, the high nitrogen evolved lines displayed increased relative fitness with decreased initial relative frequency, which suggests negative frequency dependence. Both types did not grow in the filtrate from high nitrogen evolved lines, but grew in the filtrate from low nitrogen evolved lines. However, the number of cell doublings of the high nitrogen evolved lines was three times higher than that of the low nitrogen evolved lines. One probable explanation for the negative frequency dependent fitness was that the low nitrogen evolved lines had weaker resource competitive ability and could not sufficiently use resources. Another explanation was that the high nitrogen evolved lines could use some metabolites produced by the low nitrogen evolved lines, which suggests the existence of cross-feeding interaction. Different interactions may lead to different relationships between relative fitness and initial relative frequency. Therefore, we need to account for the effects of initial relative frequency on relative fitness to more accurately measure fitness in evolutionary experiments.

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