22 Works

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...

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...

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)...

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...

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...

Numbers of individuals and endemicity for birds in three study sites of the Himalayas-Hengduan mountains of China

Yiming Hu, Brett Scheffers, Xinyuan Pan, Huijian Hu, Zhixin Zhou, Dan Liang, Cheng Wenda, Zhixin Wen & Luke Gibson
1. Describing the patterns and revealing the underlying mechanisms responsible for variations in community structure remains a central focus in ecology. However, important gaps remain, including our understanding of species abundance. Most studies on abundance-based relationships are from either temperate ecosystems or tropical ecosystems, and few have explicitly tested abundance-based relationships across a temperate to tropical ecotone. 2. Here, we use a comprehensive dataset of breeding birds across elevation spanning a temperate to subtropical gradient...

Effects of inoculation concentration, photoperiod and temperature on growth, conidiation and conidial germination of Bionectria ochroleuca

Yi Zheng, Yichun Xie, Yan Xie & Shixiao Yu
The short-term stock of Bionectria ochroleuca ochroleuca at 4°C was activated, sub-cultured, and grown at 25°C on PDA medium for 10 days to obtain a working culture. To determine the effect of temperature on fungal growth, the plates were incubated at 15, 20, 25, and 30°C under continuous darkness or an 8 h light/16 h dark regime for 10 days. To investigate the effect of photoperiod on fungal growth and reproduction, fungal cultures were incubated...

Divergent responses of symbiotic and asymbiotic N2 fixation to seawater additions

Xibin Sun, Dejun Li, Hao Chen, Zilong Ma, Kongcao Xiao, Junhua Yan, Zhenchuang Wang & Pengpeng Duan
Sea level rise-associated seawater intrusion exerts substantial impacts on the structure and function of coastal ecosystems. As nitrogen (N) availability is closely related to the structure and function of ecosystems, it is crucial to understand how seawater intrusion impacts biological N2 fixation, a major pathway of new N input to natural ecosystems. Here, a seawater addition experiment with two N2-fixing plant species (Acacia auriculiformis and Casuarina equisetifolia) and ten non-N2-fixing plant species was conducted to...

Seasonal variation in community composition and distributional ranges of birds along a subtropical elevation gradient in China

Dan Liang, Xinyuan Pan, Xu Luo, Cheng Wenda, Yanyan Zhao, Yiming Hu, Scott Robinson & Yang Liu
Aim Seasonal variation in community composition and species distributional ranges along elevational gradients remain poorly known but are essential to inform conservation. In this study, we aim to understand how species richness, community composition, and elevational ranges of montane birds change between the breeding and the non-breeding season. Location The east slope of the southern Gaoligong Mountains, Yunnan, southwestern China, elevational range: 700 - 3400 m a.s.l.; latitudinal range: 24°56´- 26°09´ N. Methods We compared...

Genome, annotations and SNPs for the green peafowl and associated scripts

Feng Dong, Hao-Chih Kuo, Guo-Ling Chen, Fei Wu, Peng-Fei Shan, Jie Wang, De Chen, Chih-Ming Hung, Yang Liu & Xiao-Jun Yang
Both anthropogenic impacts and historical climate change could contribute to population decline and species extinction, but their relative importance has yet to be determined. Emerging approaches based on genomic, climatic and anthropogenic data provide a promising analytical framework to address this question. This study applied such an integrative approach to examine potential drivers for endangerment of the green peafowl (Pavo muticus). Several demographic reconstructions based on population genomes congruently retrieved a drastic population declination since...

Plotting receiver operating characteristic and precision-recall curves from presence and background data

Wenkai Li & Qinghua Guo
The receiver operating characteristic (ROC) and precision-recall (PR) plots have been widely used to evaluate the performances of species distribution models. Plotting the ROC/PR curves requires a traditional test set with both presence and absence data (namely PA approach), but species absence data are usually not available in reality. Plotting the ROC/PR curves from presence-only data while treating background data as pseudo absence data (namely PO approach) may provide misleading results. In this study we...

Convergent and divergent brain structural and functional abnormalities associated with developmental dyslexia

Xiaohui Yan
Brain abnormalities in the reading network have been repeatedly reported in individuals with developmental dyslexia (DD); however, it is still not totally understood where the structural and functional abnormalities are consistent/inconsistent across languages. In the current multimodal meta-analysis, we found convergent structural and functional alterations in the left superior temporal gyrus across languages, suggesting a neural signature of DD. We found greater reduction in grey matter volume and brain activation in the left inferior frontal...

Genome annotation of humpback grouper (Cromileptes altivelis)

Yang Yang
Humpback grouper (Cromileptes altivelis), an Epinephelidae species, is patchily distributed in reef habitats of Western Pacific water. This grouper possesses a remarkably different body shape and notably low growth rates compared to closely related grouper species. Up to now, the evolutionary status of humpback grouper is ambiguous in grouper species. In order to promote further research of the grouper, in the present study, a high-quality chromosome-level genome of humpback grouper was assembled using PacBio sequencing...

Global resorption efficiencies of trace elements in leaves of terrestrial plants

Hao Chen, Sasha Reed, Xiao-Tao Lü, Kongcao Xiao, Kelin Wang & Dejun Li
1. Leaf nutrient resorption is a critical nutrient conservation strategy. Previous studies focus mainly on resorption patterns of macronutrients, but resorption patterns of trace elements remain poorly understood. 2. A meta-analysis was conducted to explore the general patterns of the leaf resorption of eight trace elements [i.e., copper (Cu), molybdenum (Mo), zinc (Zn), boron (B), manganese (Mn), sodium (Na), aluminum (Al), and iron (Fe)], and a macronutrient [i.e., sulfur (S)] using data collected from 53...

Relationships between plant-soil feedbacks and functional traits

Nianxun Xi, Peter Adler, Dongxia Chen, Hangyu Wu, Jane Catford, Peter Van Bodegom, Michael Bahn, Kerri Crawford & Chengjin Chu
Plant-soil feedbacks (PSF) and functional traits are two active but not well theoretically integrated areas of research. However, PSF and traits are both affected by life history evolution, so the two should theoretically be related. We provide a conceptual framework to link plant functional traits to two types of PSF metrics, and hypothesize that individual PSF (plant performance in conspecific versus heterospecific soil) should be related to the fast-slow trait spectrum, while pairwise PSF (the...

Mycorrhizal effects on decomposition and soil CO2 flux depend on changes in nitrogen availability during forest succession

Ruiqiang Liu, Yanghui He, Guiyao Zhou, Junjiong Shao, Lingyan Zhou, Huimin Zhou, Nan Li, Bingqian Song, Chao Liang, Enrong Yan, Xiao-Yong Chen, Xihua Wang, Minhuang Wang, Shahla Hosseini Bai, Xuhui Zhou & Richard Phillips
Mycorrhizal fungi play a central role in plant nutrition and nutrient cycling, yet our understanding on their effects on free-living microbes, soil carbon (C) decomposition and soil CO2 fluxes remains limited. Here we used trenches lined with mesh screens of varying sizes to isolate mycorrhizal hyphal effects on soil C dynamics in subtropical successional forests. We found that the presence of mycorrhizal hyphae suppressed soil CO2 fluxes by 17% in early-successional forests, but enhanced CO2...

Plastome and RAD-seq of Polygonatum odoratum

Shiou Yih Lee
Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, P. odoratum and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivars were observed. For genetic aspect, the plastid genome of P. odoratum varies in length from 154,569 bp to...

Community-wide trait means and variations affect biomass in a biodiversity experiment with tree seedlings

Shan Luo, Bernhard Schmid, Cameron Wagg, Yuxin Chen, Bin Jiang, Minxia Liang, Xubing Liu & Shixiao Yu
The structure of a plant community in terms of functional traits can strongly affect community productivity. Two components may contribute to this, community-wide trait means (mass-ratio hypothesis) or community-wide trait variations (diversity hypothesis) across species and individuals. We compared the explanatory power of the two hypotheses for explaining biomass variation among individuals and communities as measures of productivity. We set up experimental communities of tree seedlings that ranged in species richness from 1‒8. We measured...

Species packing and the latitudinal gradient in local beta-diversity

Ke Cao, Richard Condit, Xiangcheng Mi, Lei Chen, Wubing Xu, David F. R. P. Burslem, Chunrong Cai, Min Cao, Li-Wan Chang, Chengjin Chu, Hu Du, Sisira Ediriweera, C. S. V. Gunatilleke, I. U. A. N. Gunatilleke, Zhanqing Hao, Jinbo Li, Guangze Jin, Buhang Li, Yankun Liu, Yide Li, Michael J. O'Brien, Xiujuan Qiao, Hongwei Ni, Guochun Shen, Xihua Wang … & Jens-Christian Svenning
The decline in species richness at higher latitudes is among the most fundamental patterns in ecology. Whether changes in species composition across space (beta-diversity) contribute to this gradient of overall local species richness (gamma diversity) remains hotly debated. Previous studies that failed to resolve the issue suffered from a well-known tendency for small samples in areas with high gamma-diversity to have inflated measures of beta-diversity. We provide here a novel analytical test, using beta-diversity metrics...

Mechanisms underlying altitudinal and horizontal range contraction: The western black crested gibbon

Li Yang, Kai-Chong Shi, Chi Ma, Guo-Peng Ren & Peng-Fei Fan
Aim: Species ranges in mountain areas may shift both horizontally and altitudinally, resulting from climate change and anthropogenic impact. Two hypotheses (the abundant center hypothesis and the contagion hypothesis) have been proposed to account for patterns of horizontal range contraction. However, undulating topograph causes a mosaic of unsuitable habitats, which may complicate the spatial pattern of range contraction. We develop a framework incorporating horizontal and altitudinal range contraction patterns of a species living in mountain...

Data from: Effects of climate and topography on the diversity anomaly of plants disjunctly distributed in eastern Asia and eastern North America

Xue Yin, Hong Qian, Xinghua Sui, Minhua Zhang, Lingfeng Mao, Jens-Christian Svenning, Robert E. Ricklefs & Fangliang He
Aim: Differences in physiography have been proposed to explain the diversity anomaly for vascular plants between environmentally similar regions of eastern Asia (EAS) and eastern North America (ENA). Here, we use plant species within disjunct genera to examine whether differences in topography contribute to the diversity anomaly and whether the richness–environment relationships differ between regions. Disjuncts are used to ensure that the diversity anomaly relates to post-disjunction evolution and diversification rather than regional differences in...

An integrated phylogenetic reassessment of the parasitoid superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) results in a revised familial classification

Chen Huayan, Lahey Zachary, Elijah J. Talamas, Alejandro A. Valerio, Ovidiu A. Popovici, Luciana Musetti, Hans Klompen, Andrew Polaszek, Lubomír Masner, Andrew D. Austin & Norman F. Johnson
The superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) is a diverse group of parasitoid wasps that attack nine orders of insects as well as spiders. They appear to show a clear pattern of host group specificity among genera. A robust phylogeny is essential to understanding the monophyly of and relationships among lower level groups and the pattern of the shifts among host groups. We conducted phylogenetic analyses of Platygastroidea based on four molecular markers (18S, 28S, COI, and...

Registration Year

  • 2021
    22

Resource Types

  • Dataset
    22

Affiliations

  • Sun Yat-sen University
    22
  • Chinese Academy of Sciences
    5
  • East China Normal University
    3
  • Princeton University
    2
  • Aarhus University
    2
  • Beijing Normal University
    2
  • University of Florida
    2
  • Southern University of Science and Technology
    2
  • University of Adelaide
    1
  • Zhejiang University
    1