258 Works

Data from: Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly

Yan-Jie Feng, Qing-Feng Liu, Meng-Yun Chen, Dan Liang & Peng Zhang
In phylogenetics and population genetics, a large number of loci are often needed to accurately resolve species relationships. Normally, loci are enriched by PCR and sequenced by Sanger sequencing, which is expensive when the number of amplicons is large. Next-generation sequencing (NGS) techniques are increasingly used for parallel amplicon sequencing, which reduces sequencing costs tremendously, but has not reduced preparation costs very much. Moreover, for most current NGS methods, amplicons need to be purified and...

Data from: The genetic basis of population fecundity prediction across multiple field populations of Nilaparvata lugens

Zhong Xiang Sun, Yi Fan Zhai, Jian Qing Zhang, Kui Kang, Jing Heng Cai, Yonggui Fu, Jie Qi Qiu, Jia Wei Shen & Wen Qing Zhang
Identifying the molecular markers for complex quantitative traits in natural populations promises to provide novel insight into genetic mechanisms of adaptation and to aid in forecasting population dynamics. In this study, we investigated single nucleotide polymorphisms (SNPs) using candidate gene approach from high- and low-fecundity populations of the brown planthopper (BPH) Nilaparvata lugens Stål (Hemiptera: Delphacidae) divergently selected for fecundity. We also tested whether the population fecundity can be predicted by a few SNPs. Seven...

Data from: Sex differences in parental care: gametic investment, sexual selection and social environment

András Liker, Robert P. Freckleton, Vladimir Remes & Tamás Székely
Male and female parents often provide different type and amount of care to their offspring. Three major drivers have been proposed to explain parental sex roles: (i) differential gametic investment by males and females that precipitates into sex difference in care, (ii) different intensity of sexual selection acting on males and females, and (iii) biased social environment that facilitates the more common sex to provide more care. Here we provide the most comprehensive assessment of...

Data from: Neoadjuvant and concurrent chemotherapy have varied impacts on the prognosis of patients with the ascending and descending types of nasopharyngeal carcinoma treated with intensity-modulated radiotherapy

Ji-Jin Yao, Guan-Qun Zhou, Fan Zhang, Wang-Jian Zhang, Li Lin, Ling-Long Tang, Yan-Ping Mao, Jun Ma & Ying Sun
Purpose: To compare the outcomes of patients with ascending type (T4&N0-1) and descending type (T1-2&N3) of nasopharyngeal carcinoma (NPC) treated with concurrent chemoradiotherapy (CCRT), neoadjuvant chemotherapy (NACT) + intensity-modulated radiotherapy (RT) or NACT + CCRT. Methods: Retrospective analysis of 839 patients with ascending or descending types of NPC treated at a single institution between October 2009 to February 2012. CCRT was delivered to 236 patients, NACT + RT to 302 patients, and NACT + CCRT...

Data from: How much do phenotypic plasticity and local genetic variation contribute to phenotypic divergences along environmental gradients in widespread invasive plants? A meta-analysis

Huixuan Liao, Carla M. D'Antonio, Baoming Chen, Qiaoqiao Huang & Shaolin Peng
For introduced species that have spread across a wide distributional range, phenotypic plasticity (PLA) has often been proposed as an important contributor to invasion success, because it increases the survival rate during initial colonization. In contrast, local genetic variation (LOC) has also been proposed to be important, because it could allow invaders to evolve high performance in a new habitat. While evolutionary ecologists have long been interested in understanding genetic mechanisms that allow rapid colonization...

Data from: Abundance-dependent effects of neighborhood dissimilarity and growth rank reversal in a Neotropical forest

Yuxin Chen, María Natalia Umaña, María Uriarte & Shixiao Yu
Why tropical forests harbor an exceptional number of species with striking differences in abundances remains an open question. We propose a theoretical framework to address this question in which rare species may have different extirpation risks depending on species ranks in tree growth and sensitivities to neighborhood interactions. To evaluate the framework, we studied tree growth and its responses to neighborhood dissimilarity (ND) in traits and phylogeny for 146 species in a Neotropical forest. We...

Freeze-tolerance of poleward-spreading mangrove species weakened by soil properties of resident salt marsh competitor

Enjian Chen, Julie Blaze, Rachel Smith, Shaolin Peng & James Byers
1. Background: Increasing temperatures associated with climate change are shifting plant species to higher latitudes. Soil communities could aid the plants’ shift into novel areas by harbouring fewer soil-borne antagonists or more mutualists that influence the fitness and stress tolerance of the shifting species. Alternatively, they could contain novel antagonists or fewer mutualists. Thus, soil communities could positively or negatively affect plant range expansion, particularly if they influence plants’ responses to climate, such as freeze...

Data from: A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry

Yuan Zhang, SiYao Huang, Dan Liang, HuoShuai Wang & Peng Zhang
The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences,...

Data from: Species colonisation, not competitive exclusion, drives community overdispersion over long-term succession

Shao-Peng Li, Marc W. Cadotte, Scott J. Meiners, Zheng-Shuang Hua, Lin Jiang & Wen-Sheng Shu
Ecological communities often transition from phylogenetic and functional clustering to overdispersion over succession as judged by space-for-time substitution studies. Such a pattern has been generally attributed to the increase in competitive exclusion of closely related species with similar traits through time, although colonisation and extinction have rarely been examined. Using 44 years of uninterrupted old-field succession in New Jersey, USA, we confirmed that phylogenetic and functional clustering decreased as succession unfolded, but the transition was...

Data from: Soil biota suppress positive plant diversity effects on productivity at high but not low soil fertility

Shan Luo, Gerlinde B. De Deyn, Bin Jiang & Shixiao Yu
1. Plant community productivity commonly increases with increasing plant diversity, which is explained by complementarity among plant species in resource utilization (complementarity effect), or by selection of particularly productive plant species in diverse plant communities (selection effect). Recent studies have also shown that soil biota can drive the positive plant diversity–productivity relationship by suppressing productivity more in low- than in high-diversity plant communities. However, much remains unknown about whether soil fertility plays a role in...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

Data from: Study on the optimization of the deposition rate of planetary GaN-MOCVD films based on CFD simulation and the corresponding surface model

Jian Li, Ze-Yuan Fei, Yi-Feng Xu, Jie Wang, Bing-Feng Fan, Xue-Jin Ma & Gang Wang
Metal-organic chemical vapour deposition (MOCVD) is a key technique for fabricating GaN thin film structures for light-emitting and semiconductor laser diodes. Film uniformity is an important index to measure equipment performance and chip processes. This paper introduces a method to improve the quality of thin films by optimizing the rotation speed of different substrates of a model consisting of a planetary with seven 6-inch wafers for the planetary GaN-MOCVD. A numerical solution to the transient...

Draft genome assemblies of Cryptolaemus montrouzieri

Hao-Sen Li
Cryptolaemus montrouzieri is a ladybird biological control agent. This data is the draft genome assemblies of C. montrouzieri.

Species responses to changing precipitation depends on trait plasticity rather than trait means and intraspecific variation

Bingwei Zhang, Yann Hautier, Xingru Tan, Cuihai You, Marc Cadotte, Chengjin Chu, Lin Jiang, Xinghua Sui, Tingting Ren, Xingguo Han & Shiping Chen
1. Trait-based approaches are key to develop mechanistic understanding of differences in plant species performance under environmental change. While mean trait values have been widely used to link functional traits to species performance, the contribution of intraspecific trait variation and trait plasticity remains unclear. Moreover, environmentally induced changes in species biomass is caused by changes in the number of individuals and individual growth rate, both of which should be influenced by trait differences and plasticity....

Plot-level wood-leaf separation for terrestrial laser scanning point clouds

Peng Wan, Wuming Zhang & Shuangna Jin
With the increasing use of terrestrial laser scanning (TLS) technology in the field of forest ecology, wood-leaf separation for TLS point clouds of forest plots has attracted a large number of studies. This dataset was open to the public for the developing, testing and comparision of the wood-leaf separation methods for TLS data. The dataset was collected from three forest plots of different stem density, topography and tree species, i.e., a white birch (Betula papyrifera)...

Expression and comparison of unigene in the transcriptome in Siniperca chuatsi

Guifeng Li
Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. After screening, 39005 unigenes were annotated into four databases, including Nr (38833, 52.9%), Swissprot (337479, 46.0%), COG (10926, 14.8%) and KEGG (19791, 26.9%). Finally, the results was annotated by Nr database which defined the maximum number of unigenes.

A dormant amoeba species can selectively sense and predate on different soil bacteria

Longfei Shu, Zhenzhen He, Xiaotong Guan, Xueqin Yang, Yuehui Tian, Siyi Zhang, Chenyuan Wu, Zhili He, Qingyun Yan, Cheng Wang & Yijing Shi
1. Soil protists are the invisible majority of soil eukaryotes, which are essential but often forgotten parts of the soil ecosystem. They play key roles in microbial food webs by predating on other soil microbes. However, it is not clear how dormant soil protists sense, recognize and feed on diverse microbial preys. 2. In this study, we used a soil amoeba, Dictyostelium discoideum, to study selective discrimination and predation of 14 different bacteria. We found...

Annotation of genome of brown-marbled grouper (Epinephelus fuscoguttatus)

Yang Yang, Lina Wu, Jingfang Chen, Xi Wu, Weiwei Zhang, Jian Luo, Junhong Xia, Zining Meng & Xiaochun Liu
Brown-marbled grouper (Epinephelus fuscoguttatus) is an important fish species for coral reef ecosystem and marine aquaculture industry. In the study, a high quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximate 42% and 0.35 %, respectively in brown-marbled grouper genome. A total of 230 contigs with total length of 1,047 Mb were assembled, contig N50 was 13.8 Mb, 228 contigs (99.13%) can...

Evolution of social organization: phylogenetic analyses of ecology and sexual selection in weavers

Zitan Song
Crook published a landmark study on the social organization of weavers (or weaverbirds, family Ploceidae) that contributed to the emergence of sociobiology, behavioral ecology, and phylogenetic comparative methods. By comparing ecology, spatial distribution, and mating systems, Crook suggested that the spatial distribution of food resources and breeding habitats influence weaver aggregation, both during the breeding season (colonial vs solitary breeding) and non-breeding season (flocking vs solitary foraging), and the food resources distribution and breeding aggregation...

Protein disulfide isomerases (PDIs) negatively regulate ebolavirus structural glycoprotein expression in the endoplasmic reticulum (ER) via the autophagy-lysosomal pathway

Bin Wang, Jing Zhang, Xin Liu, Qingqing Chai, Xiaoran Lu, Xiaoyu Yao, Zhichang Yang, Liangliang Sun, Silas F. Johnson, Richard C Schwartz & Yong-Hui Zheng
Zaire ebolavirus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates with high morbidity and mortality. EBOV infection is dependent on its structural glycoprotein (GP), but high levels of GP expression also trigger cell rounding, detachment, and downregulation of many surface molecules that is thought to contribute to its high pathogenicity. Thus, EBOV has evolved an RNA editing mechanism to reduce its GP expression and increase its fitness. We now report that the...

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li & Ming-Qing Li
Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated...

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li & Ming-Qing Li
Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated...

Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China

Xiaomeng Mao, Zixiao Guo, Xie Wei, Xinnian Li, Suhua Shi & Zixiao Guo
Background: Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering ‘blue carbon’. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country’s coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect...

Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation

Wei Xie, Zixiao Guo, Jiayan Wang, Ziwen He, Yulong Li, Xiao Feng, Cairong Zhong & Suhua Shi
How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species...

Additional file 1 of A CT-based nomogram for differentiating invasive fungal disease of the lung from bacterial pneumonia

Meilin Gong, Jingmei Xu, Kang Li, Ke Li, Yuwei Xia, Yang Jing, Jiafei Chen, Jing Li, Jing Yang, Mingshan Du, Wenjing Hou, Yuan Ou, Lian Li & Wei Chen
Additional file 1. On the orininal data of the study.

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Resource Types

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  • Sun Yat-sen University
  • Fudan University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Zhejiang University
  • Shanghai Jiao Tong University
  • Chinese Academy of Sciences
  • Sichuan University
  • Jilin University
  • University of Chinese Academy of Sciences
  • Southeast University