121 Works

Data from: Factors determining forest diversity and biomass on a tropical volcano, Mt. Rinjani, Lombok, Indonesia

Gbadamassi G. O. Dossa, Ekananda Paudel, Junichi Fujinuma, Haiying Yu, Wanlop Chutipong, Yuan Zhang, Sherryl Paz, Rhett D. Harrison & Nathan G. Swenson
Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetation over an altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modeled alpha- (plot) and beta- (among plot) diversity (Fisher’s alpha), compositional change, and biomass against elevation and selected covariates. We also examined community phylogenetic structure across the...

Data from: Responses of growing‐season soil respiration to water and nitrogen addition as affected by grazing intensity

Jianjun Li, Yin Huang, Fengwei Xu, Liji Wu, Dima Chen & Yongfei Bai
1. Most grasslands in the world, including the semi-arid steppe in China, are threatened by nitrogen deposition, precipitation change, and livestock grazing, which greatly affect soil carbon processes (e. g., soil respiration). Although the individual effects of nitrogen deposition and precipitation change on soil respiration are well understood, how their effects on soil respiration are altered by different grazing intensities is unclear. 2. To determine how the effects of nitrogen deposition and precipitation change on...

Data from: Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

Zi-Min Hu, Jing-Jing Li, Zhong-Min Sun, Jung-Hyun Oak, Jie Zhang, Pablo Fresia, W. Stewart Grant & De-Lin Duan
A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from...

Data from: Population genetic structure of Oryza rufipogon and O. nivara: implications for the origin of O. nivara

Rong Liu, Xiao-Ming Zheng, Lian Zhou, Hai-Fei Zhou & Song Ge
Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains...

Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features

Hui Wu, Zhen Ma, Ming-Ming Wang, Ai-Li Qin, Jin-Hua Ran & Xiao-Quan Wang
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here we investigate the origin and evolution of polyploids of Ephedra distributed in the Qinghai-Tibetan Plateau (QTP) and neighboring areas. Flow cytometry (FCM) was used to measure the...

Data from: Simple parameterization of aerodynamic roughness lengths and the turbulent heat fluxes at the top of midlatitude August‐one glacier, Qilian Mountains, China

Shuhai Guo, Rensheng Chen, Guohua Liu, Chuntan Han, Yaoxuan Song, Junfeng Liu, Yong Yang, Zhangwen Liu, Xiqiang Wang, Xiaojiao Liu, Lei Wang & Qin Zheng
The fluxes of sensible heat (H) and latent heat (LE), which are generally the important parts of the energy and mass balances over glacier surfaces, are widely quantified by the bulk method. However, due to the difficulty of determining the aerodynamic roughness length z0m in this method, H and LE values may still have large uncertainties with significant inaccuracy. To acquire reliable varying and intrinsic z0m values, new simpler parameterizations for z0m values at different...

Data from: Spatial variation of soil respiration in a cropland under winter wheat and summer maize rotation in the North China Plain

Ni H. Huang, Li Wang, Yongsen Hu, Haifeng Tian & Zheng Niu
Spatial variation of soil respiration (Rs) in cropland ecosystems must be assessed to evaluate the global terrestrial carbon budget. This study aims to explore the spatial characteristics and controlling factors of Rs in a cropland under winter wheat and summer maize rotation in the North China Plain. We collected Rs data from 23 sample plots in the cropland. At the late jointing stage, the daily mean Rs of summer maize (4.74 μmol CO2 m-2 s-1)...

Data from: Stream diatoms exhibit weak niche conservation along global environmental and climatic gradients

Janne Soininen, Aurelien Jamoneau, Juliette Tison-Rosebery, Thibault Leboucher, Jianjun Wang, Mikolaj Kokocinski & Sophia I. Passy
Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whether NC was evident in stream diatom morphospecies by modeling species responses to environmental and climatic variables in a set of calibration sites (from the US) and then evaluated the models with...

Data from: Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

Li-Na Zhang, Xian-Zhi Zhang, Yu-Xiao Zhang, Chun-Xia Zeng, Peng-Fei Ma, Lei Zhao, Zhen-Hua Guo & De-Zhu Li
The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared to...

Data from: Home-field advantages of litter decomposition increase with increasing N deposition rates: a litter and soil perspective

Ying-Bin Li, Qi Li, Jun-Jie Yang, Xiao-Tao Lv, Wen-Ju Liang, Xing-Guo Han & T. Martijn Bezemer
1. Differences in litter quality and in soil microbial community composition can influence the litter decomposition and “home-field advantage” (HFA). However, our knowledge about the relative role of litter and soil characteristics on litter decomposition and HFA effects is still limited, especially under long-term N deposition. 2. We collected soil and two types of litter (monospecific and mixed species litter) from five replicate plots from a long-term N-deposition field experiment with seven N-addition treatments (0,...

Data from: Allocation strategies for nitrogen and phosphorus in forest plants

Jiahui Zhang, Nianpeng He, Congcong Liu, Li Xu, Qiang Yu & GuiRui Yu
The allocation of limiting elements, such as nitrogen (N) and phosphorus (P), in plants is an important basis for structural stability and functional optimization in natural plant communities. However, because of the lack of systematic investigation data, the mechanisms of optimal nutrient allocation in plants in natural forests are still unclear. Using consistent measurements of N and P contents in 930 plant species, we explored the allocation strategies for N and P in different plant...

Data from: Congruent species delimitation of two controversial gold-thread nanmu tree species based on morphological and restriction site-associated DNA sequencing data

Xin Ding, Jianhua Xiao, Lang Li, John G Canran, Jie Li, John G. Conran & Jian Hua Xiao
Species delimitation is fundamental to conservation and sustainable use of economically important forest tree species. However, the delimitation of two highly valued gold-thread nanmu species (Phoebe bournei and P. zhennan) has been confusing and debated. To address this problem, we integrated morphology and restriction site-associated DNA sequencing (RADseq) to define their species boundaries. We obtained highly consistent results from both data sets, supporting two distinct lineages corresponding to P. bournei and P. zhennan. In Phoebe...

Data from: Testing the scaling effects and mechanisms of N-induced biodiversity loss: evidence from a decade-long grassland experiment

Zhichun Lan, G. Darrel Jenerette, Shuxia Zhan, Wenhuai Li, Shuxia Zheng & Yongfei Bai
Although extensive studies demonstrate that nitrogen (N) enrichment frequently reduces plant diversity within small quadrats (0.5 –4 m2), only a few studies have evaluated N effects on biodiversity across different spatial scales. We conducted the first experimental test of the scale dependence of N effects on species richness from a 10-year N treatment (1.75- 28 g N m−2 yr−1) in a typical steppe. We used species area relationship (SAR) to analyze the scale dependence of...

Data from: Structure of the epiphyte community in a tropical montane forest in SW China

Mingxu Zhao, Nalaka Geekiyanage, Jianchu Xu, Myo Myo Khin, Dian Ridwan Nurdiana, Ekananda Paudel & Rhett Daniel Harrison
Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site...

Data from: Comparative transcriptome resources of eleven Primulina species, a group of “stone plants” from a biodiversity hotspot

Bin Ai, Yong Gao, Xiaolong Zhang, Junjie Tao, Ming Kang & Hongwen Huang
The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an...

Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

Lemian Liu, Min Liu, David M. Wilkinson, Huihuang Chen, Xiaoqing Yu & Yang Jun
Microeukaryotic plankton (0.2–200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve –by using...

Data from: Divergence in strategies for coping with winter embolism among co-occurring temperate tree species: the role of positive xylem pressure, wood type and tree stature

Cun-Yang Niu, Frederick C. Meinzer & Guang-You Hao
1. In temperate ecosystems, freeze-thaw events are an important environmental stress that can induce severe xylem embolism (i.e. clogging of conduits by air bubbles) in overwintering organs of trees. However, no comparative studies of different adaptive strategies among sympatric tree species for coping with winter embolism have examined the potential role of the presence or absence of embolism refilling by positive xylem pressure. 2. We evaluated the degree of winter embolism and hydraulic architecture traits...

Data from: Long-term antagonistic effect of increased precipitation and nitrogen addition on soil respiration in a semiarid steppe

Hongyan Han, Yue Du, Dafeng Hui, Lin Jiang, Mingxing Zhong & Shiqiang Wan
Changes in water and nitrogen (N) availability due to climate change and atmospheric N deposition could have significant effects on soil respiration, a major pathway of carbon (C) loss from terrestrial ecosystems. A manipulative experiment simulating increased precipitation and atmospheric N deposition has been conducted for 9 years (2005–2013) in a semiarid grassland in Mongolian Plateau, China. Increased precipitation and N addition interactively affect soil respiration through the 9 years. The interactions demonstrated that N...

Data from: Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055

Yanlei Fu, Hailing Ma, Siying Chen, Tianyu Gu & Jiming Gong
Proline plays a crucial role in the drought stress response in plants. However, there are still gaps in our knowledge about the molecular mechanisms that regulate proline metabolism under drought stress. Here, we report that the histone methylase encoded by CAU1, which is genetically upstream of P5CS1 (encoding the proline biosynthetic enzyme Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in proline-mediated drought tolerance. We determined that the transcript level of CAU1 decreased while that of...

Does land use age influence carbon cycling in the Tibetan Plateau?

Meta Francis Justine, Pan Kaiwen, Nambajimana Jean De Dieu, Fidele Karamage, Zebene Tadesse, Bikram Pandey, Yang Wanqin, Wu Fuzhong, Olusanya Abioudun Olatunji, Nirdesh Nepal, Friday Uchege, Akash Tariq, Lin Zhang & Xiaoming Sun
Although substantial information had been generated on the effects of land use change on soil organic carbon (SOC) and total nitrogen (TN) storage, studies are absent on multifactorial effects of land use types, land use age, and elevation on SOC and TN storage. SOC and TN were therefore investigated in 30 field sites comprising natural forests, planted forests, shrub, and grasslands. SOC and TN stocks differed and correlated significantly with land use age; the C...

Biomass allocation and productivity–richness relationship across four grassland types at the Qinghai Plateau

Licong Dai, Xiaowei Guo, Xun Ke, Yuting Lan, Fawei Zhang, Yikang Li, Li Lin, Qian Li, Guangmin Cao, Bo Fan, Dawen Qian, Huakun Zhou & Yangong Du
Aboveground biomass (AGB) and belowground biomass (BGB) allocation and productivity–richness relationship are controversial. Here, we assessed AGB and BGB allocation and the productivity–richness relationship at community level across four grassland types based on the biomass data collected from 80 sites across the Qinghai Plateau during 2011–2012. The reduced major axis regression and general linear models were used and showed that (1) the median values of AGB were significantly higher in alpine meadow than in other...

Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques

Chao Xu, Wenpan Dong, Shi Shuo, Cheng Tao, Changhao Li, Yanlei Liu, Ping Wu, Honghun Wu, Peng Gao & Shiliang Zhou
A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA...

Data from: Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set

Wenpan Dong, Tao Cheng, Changhao Li, Chao Xu, Ping Long, Chunming Chen & Shiliang Zhou
The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analyzing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region...

Data from: High-throughput monitoring of wild bee diversity and abundance via mitogenomics

Min Tang, Chloe J. Hardman, Yinqiu Ji, Guanliang Meng, Shanlin Liu, Meihua Tang, Shenzhou Yang, Ellen D. Moss, Jiaxin Wang, Chenxue Yang, Catharine Bruce, Tim Nevard, Simon G. Potts, Xin Zhou, Douglas W. Yu & Meihua Tan
1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and...

Data from: Microsatellite evidence for high frequency of multiple paternity in the marine gastropod Rapana venosa

Dongxiu Xue, Tao Zhang, Liu Jin-Xian & Jin-Xian Liu
Background: Inferring of parentage in natural populations is important in understanding the mating systems of a species, which have great effects on its genetic structure and evolution. Muricidae, a large group (approximately 1,600 species) of marine gastropods, are poorly investigated in patterns of multiple paternity and sperm competition based on molecular techniques. The veined Rapa whelk, Rapana venosa, a commercially important muricid species with internal fertilization, is an ideal species to study the occurrence and...

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