40 Works

Data from: Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in Southeast Asia

Yan-Yan Guo, Yi-Bo Luo, Zhong-Jian Liu & Xiao-Quan Wang
South-East Asia covers four of the world's biodiversity hotspots, showing high species diversity and endemism. Owing to the successive expansion and contraction of distribution and the fragmentation by geographical barriers, the tropical flora greatly diversified in this region during the Tertiary, but the evolutionary tempo and mode of species diversity remain poorly investigated. Paphiopedilum, the largest genus of slipper orchids comprising nearly 100 species, is mainly distributed in South-East Asia, providing an ideal system for...

Data from: Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests

Junjun Ding, Yuguang Zhang, Mengmeng Wang, Xin Sun, Jing Cong, Ye Deng, Hui Lu, Tong Yuan, Joy D. Van Nostrand, Diqiang Li, Jizhong Zhou & Yunfeng Yang
As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as ‘The Oriental...

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: 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: A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings

Xing Xu, Xiaoting Zheng, Corwin Sullivan, Xiaoli Wang, Lida Xing, Yan Wang, Xiaomei Zhang, Jingmai K. O'Connor, Fucheng Zhang & Yanhong Pan
The wings of birds and their closest theropod relatives share a uniform fundamental architecture, with pinnate flight feathers as the key component. Here we report a new scansoriopterygid theropod, Yi qi gen. et sp. nov., based on a new specimen from the Middle–Upper Jurassic period Tiaojishan Formation of Hebei Province, China. Yi is nested phylogenetically among winged theropods but has large stiff filamentous feathers of an unusual type on both the forelimb and hindlimb. However,...

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: Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism

Enwei Tian, John D. Nason, Linna Zheng, Hui Yu, Finn Kjellberg & Carlos A. Machado
Historical abiotic factors such as climatic oscillations and extreme climatic events as well as biotic factors have shaped the structuring of species’ genetic diversity. In obligate species-specific mutualisms, the biogeographic histories of the interacting species are tightly linked. This could be particularly true for nuclear genes in the Ficus-pollinating wasp mutualistic association as the insects disperse pollen from their natal tree. In this study we compare spatial genetic structure of plant and pollinator for the...

Data from: Does mixed-species flocking influence how birds respond to a gradient of land-use intensity?

Christos Mammides, Jin Chen, Uromi Manage Goodale, Sarath Wimalabandara Kotagama, Swati Sidhu & Eben Goodale
Conservation biology is increasingly concerned with preserving interactions among species such as mutualisms in landscapes facing anthropogenic change. We investigated how one kind of mutualism, mixed-species bird flocks, influences the way in which birds respond to different habitat types of varying land-use intensity. We use data from a well-replicated, large-scale study in Sri Lanka and the Western Ghats of India, in which flocks were observed inside forest reserves, in ‘buffer zones' of degraded forest or...

Data from: Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation biogeography and reticulate evolution

Jie Wu, Tommi Nyman, Dong-Chao Wang, George W. Argus, Yong-Ping Yang & Jia-Hui Chen
Background The taxonomy and systematics of Salix subgenus Salix s.l. is difficult. The reliability and evolutionary implications of two important morphological characters (number of stamens, and morphology of bud scales) used in subgeneric classification within Salix remain untested, and a disjunct Old–New World distribution pattern of a main clade of subgenus Salix s.l., revealed by a previous study, lacks a reasonable explanation. To study these questions, we conducted phylogenetic analyses based on 4,688 bp of...

Data from: Increased sensitivity of DNA damage response-deficient cells to stimulated microgravity-induced DNA lesions

Nan Li, Lili An & Haiying Hang
Microgravity is a major stress factor that astronauts have to face in space. In the past, the effects of microgravity on genomic DNA damage were studied, and it seems that the effect on genomic DNA depends on cell types and the length of exposure time to microgravity or simulated microgravity (SMG). In this study we used mouse embryonic stem (MES) and mouse embryonic fibroblast (MEF) cells to assess the effects of SMG on DNA lesions....

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex

Yaping Lin, Yiyong Chen, Wei Xiong & Aibin Zhan
The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genome-wide genetic markers are still lacking. Here we characterized a large set of genome-wide gene-associated microsatellite markers for C. intestinalis spA (= C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based...

Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)

Bai-Dong Zhang, Dong-Xiu Xue, Juan Wang, Yu-Long Li, Bing-Jian Liu & Jin-Xian Liu
Recent advances in high-throughput sequencing technologies have offered the possibility to generate genome-wide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters, and to evaluate potential adaptive divergence. Here, we identified 27 556 single-nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation was identified, with an average nucleotide diversity (π) of 0.00105 ±...

Data from: Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant

Sergei Volis, Danara Ormanbekova, Kanat Yermekbayev, Saule Abugalieva, Yerlan Turuspekov & Irina Shulgina
Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, human made changes in the natural environment pose a new context to this issue, i.e. adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the...

Data from: Morphometric traits capture the climatically driven species turnover of 10 spruce taxa across China

He Li, Guohong Wang, Yun Zhang & WeiKang Zhang
This study explored the relative roles of climate and phylogenetic background in driving morphometric trait variation in 10 spruce taxa in China. The study further addressed the hypothesis that these variations are consistent with species turnover on climatic gradients. Nine morphometric traits of leaves, seed cones, and seeds for the 10 studied spruce taxa were measured at 504 sites. These data were analyzed in combination with species DNA sequences from NCBI GenBank. We detected the...

Data from: Subordinate plants sustain the complexity and stability of soil micro-food webs in natural bamboo forest ecosystems

Yuanhu Shao, Xiaoli Wang, Jie Zhao, Jianping Wu, Weixin Zhang, Deborah A. Neher, Yanxia Li, Yiping Lou & Shenglei Fu
Subordinate plants have a significant impact on soil organisms in primary successional floodplains and grassland ecosystems, but their role in subtropical forest ecosystems remains unclear. An experiment was conducted in a subtropical forest to test the hypothesis that removal of shrubs or subordinate arbour tree species would reduce the complexity and stability of the soil micro-food web. Principal response curves (PRCs) were performed to assess the responses of soil microbial and nematode communities to plant...

Data from: Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)

Alex Harkess, Francesco Mercati, Hong-Yan Shan, Francesco Sunseri, Agostino Falavigna & Jim Leebens-Mack
Sex chromosomes have evolved independently in phylogenetically diverse flowering plant lineages. The genes governing sex determination in dioecious species remain unknown, but theory predicts that the linkage of genes influencing male and female function will spur the origin and early evolution of sex chromosomes. For example, in an XY system, the origin of an active Y may be spurred by the linkage of female suppressing and male promoting genes. Garden asparagus (Asparagus officinalis) serves as...

Data from: Community-wide changes in inter-taxonomic temporal co-occurrence resulting from phenological shifts

Fangyuan Hua, Junhua Hu, Yang Liu, Xingli Giam, Tien Ming Lee, Hao Luo, Jia Wu, Qiaoyi Liang, Jian Zhao, Xiaoyan Long, Hong Pang, Biao Wang, Wei Liang, Zhengwang Zhang, Xuejie Gao & Jiang Zhu
Global climate change is known to affect the assembly of ecological communities by altering species’ spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species’ temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon...

Data from: The functional significance of complex floral colour pattern in a food-deceptive orchid

Xiaokai Ma, Jun Shi, Hans Banziger, Yangna Sun, Yanyan Guo, Zhongjian Liu, Steven D. Johnson & Yibo Luo
Many non-rewarding orchid species mimic the signals of co-occurring food flowers and thereby attract food-seeking animal pollinators. These signals are often visually complex with a colour pattern that contrasts between outer and central parts. The significance of this colour complexity for the pollination success of flowers of deceptive orchids has scarcely been investigated. We tested the effects of the colour patterns of the food-deceptive orchid Paphiopedilum micranthum on bumblebee visitation choices and pollination success using...

Data from: Fewer new species colonize at low frequency N addition in a temperate grassland

Yunhai Zhang, Carly J. Stevens, Xiaotao Lü, Nianpeng He, Jianhui Huang & Xingguo Han
1. Biologically reactive nitrogen (Nr) enrichment threatens biodiversity in diverse ecosystems. Previous controlled N addition experiments may overestimate the effects of atmospheric Nr deposition on the rate of species loss, as it has been found that low frequency Nr additions, as used in traditional studies, lead to more rapid biodiversity loss. It remains unclear, however, whether the colonization of new species (gain) or extinction of old species (loss) is the cause of this difference. 2....

Data from: Correct calculation of CO2 efflux using a closed-chamber linked to a non-dispersive infrared gas analyzer

Gbadamassi G. O. Dossa, Ekananda Paudel, Hongyan Wang, Kunfang Cao, Douglas Schaefer & Rhett D. Harrison
1. Improved understanding of the carbon (C) cycle is essential to model future climates and how this may feedback to affect greenhouse-gas fluxes. 2 .We summarize previous work quantifying respiration rates of organic substrates and briefly discuss how advances in technology, specifically the use of chambers linked to a non-dispersive infra-red gas analyzer (NDIR), can be applied to assess carbon dynamics from short-term field measurements. This technology hastens measurement and is relatively inexpensive, enabling researchers...

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: 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...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Chinese Academy of Sciences
  • University of Chinese Academy of Sciences
  • World Agroforestry Centre
  • Kunming Institute of Botany
  • University of Tennessee at Knoxville
  • Tsinghua University
  • Kunming Institute of Zoology
  • Institute of Oceanology
  • Beijing Genomics Institute
  • Lancaster University