40 Works

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: 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: 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: 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: 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...

Data from: Genetic structure and post-glacial expansion of Cornus florida L. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling

Ashley Call, Yan-Xia Sun, Yan Yu, Peter B. Pearman, David T. Thomas, Robert Trigiano, Ignazio Carbone, Qiu-Yun Xiang, Robert N. Trigiano, Yan-Xia Sun & Qiu-Yun Jenny Xiang
Repeated global climatic cooling and warming cycles during the Pleistocene played a major role in the distribution and evolution of the Earth biota. Here, we integrate phylogeography, coalescent-based Bayesian estimation of demographic history, and species distribution modeling (SDM) to understand the genetic patterns and biogeography of the flowering dogwood, Cornus florida subsp. florida L., since the Last Glacial Maximum (LGM). Natural populations of the species are severely threatened by dogwood anthracnose. We genotyped 306 plants...

Data from: Mito-nuclear phylogeography of the cyprinid fish Gymnodiptychus dybowskii in the arid Tien Shan region of Central Asia

Guogang Li, Zuogang Peng, Renyi Zhang, Yongtao Tang, Chao Tong, Chenguang Feng, Cunfang Zhang & Kai Zhao
We evaluated the phylogeography and historical demography of the cyprinid fish Gymnodiptychus dybowskii (subfamily Schizothoracinae) across three northern Qinghai-Tibetan Plateau (QTP) river systems in the Tien Shan range: the Kaidu River, Ili River and Junggar Basin. Results from both mtDNA (16S rRNA and Cyt b) and nuDNA (RAG-2) resolved three reciprocally monophyletic clades, one in each of the three river basins. Estimated divergence times (highest posterior density (HPD) 2.4–3.7 Mya) are consistent with the hypothesis...

Data from: C:N:P stoichiometry of Artemisia species and close relatives across northern China: unraveling effects of climate, soil and taxonomy

Xuejun Yang, Zhenying Huang, Keliang Zhang & Johannes Hans C. Cornelissen
1. Carbon (C), nitrogen (N) and phosphorus (P) stoichiometries play critical roles in the function and structure of ecosystems by affecting important ecological processes. Yet, most studies to date have concentrated on foliar stoichiometry of phylogenetically distantly related species. 2. Here, we hypothesized that (i) plant stoichiometry of closely related species still shows biogeographic patterns because of the geographic patterns of abiotic environment at the regional scale and (ii) even related species still differ strongly...

Data from: Functional correlations between specific leaf area and specific root length along a regional environmental gradient in Inner Mongolia grasslands

Junhui Cheng, Pengfei Chu, Dima Chen & Yongfei Bai
Among above- and belowground traits, specific leaf area (SLA, cm2 g−1) and specific root length (SRL, m g−1) are the two key traits reflecting species resource acquisition strategies. However, patterns of variation in SLA and SRL have rarely been examined simultaneously across evolutionary history and environmental gradients, and the SLA-SRL relationship is still controversial on several grounds. We examined the inter- and intraspecific variations in SLA and SRL of different root branching orders and the...

Data from: Yet another empty forest: considering the conservation value of a recently established tropical nature reserve

Rachakonder Sreekar, Kai Zhang, Jianchu Xu, Rhett D. Harrison & Rachakonda Sreekar
The primary approach used to conserve tropical biodiversity is in the establishment of protected areas. However, many tropical nature reserves are performing poorly and interventions in the broader landscape may be essential for conserving biodiversity both within reserves and at large. Between October 2010 and 2012, we conducted bird surveys in and around a recently established nature reserve in Xishuangbanna, China. We constructed a checklist of observed species, previously recorded species, and species inferred to...

Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

Tao Cheng, Chao Xu, Li Lei, Changhao Li, Yu Zhang & Shiliang Zhou
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from...

Data from: Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

Camille Lepoittevin, Catherine Bodénès, Emilie Chancerel, Laure Villate, Tiange Lang, Isabelle Lesur, Christophe Boury, François Ehrenmann, Diana Zelenika, Anne Boland, Céline Besse, Pauline Garnier-Géré, Christophe Plomion & Antoine Kremer
An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5112 contigs (6542 putative in silico SNPs). The 7913 SNPs were genotyped across the six parental individuals, full-sib progenies (one within each species and two interspecific crosses between Q. petraea...

Data from: Soil acidification exerts a greater control on soil respiration than soil nitrogen availability in grasslands subjected to long-term nitrogen enrichment

Dima Chen, Jianjun Li, Zhichun Lan, Shuijin Hu & Yongfei Bai
Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide-range of impacts on biotic communities and hence on soil respiration. Reduction in below-ground carbon (C) allocation induced by high N availability has been assumed to be a major mechanism determining the effects of N enrichment on soil respiration. In addition to increasing available N, however, N enrichment causes...

Data from: Reducing soil erosion by improving community functional diversity in semi-arid grasslands

Huoxing Zhu, Bojie Fu, Shuai Wang, Linhai Zhu, Lei Jiao, Cong Wang & Liwei Zhang
1. Great efforts have been made to control soil erosion by restoring plant communities in degraded ecosystems world-wide. However, soil erosion has not been substantially reduced mainly because current restoration strategies lead to large areas of mono-specific vegetation, which are inefficient in reducing soil erosion because of their simple canopy and root structure. Therefore, an advanced understanding of how community functional composition affects soil erosion processes, as well as an improved restoration scheme to reduce...

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