54 Works

Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis

Yongshuai Sun, Richard J. Abbott, Zhiqiang Lu, Kangshan Mao, Lei Zhang, Xiaojuan Wang, Dafu Ru & Jianquan Liu
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair...

Data from: Abundance of small mammals correlates with their elevational range sizes and elevational distributions in the subtropics

Zhixin Wen, Yongjie Wu, Jilong Cheng, Tianlong Cai, Yuanbao Du, Deyan Ge, Lin Xia & Qisen Yang
The idea that a positive abundance-range size relationship (ARR) is pervasive in nature has been challenged by recent studies focused on montane and island vertebrate assemblages. However, because some of these studies used species’ local abundance and regional or global range size in examining the ARRs, the negative and neutral trends reported are questionable. Here, by relating species’ mean abundance along elevational gradients to elevational range size, we examined the ARRs of non-flying small mammals...

Data from: Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

Jialiang Li, Richard Ian Milne, Dafu Ru, Jibin Miao, Wenjing Tao, Lei Zhang, Jingjing Xu, Jianquan Liu & Kangshan Mao
Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of Cupressus chengiana , to assess population genomics across the species' full range, comprising the Daduhe River (DDH), Minjiang River (MJR) and...

Enhanced Heterogenous Hydration of SO2 Through Immobilization of Pyridinic-N on Carbon Materials

Wanglai Cen, Longhua Zou, Ping Yan, Peng Lu, Dongyao Chen & Wei Chu
Carbon materials doped with nitrogen has long been utilized for SO2 removal from flue gases for the benefits of environment. The role of water is generally regarded as hydration of SO3 which is formed through the oxidization of SO2. However, the hydrolysis of SO2, especially on the surface of N doped carbon materials, was almost ignored. In this study, the hydrolysis of SO2 was investigated in detail on the pyridinic nitrogen (PyN) doped graphene (GP)...

Daily Tourist Volume

Li Cheng
It is the daily tourist volume of Jiuzhai Valley National park, China

Data from: Pternopetalum porphyronotum sp. nov. (Apiaceae) from Sichuan, China

Yan Zhong, Bin Wang, Jia-Zhen Zhang & Jin-Bo Tan
Pternopetalum porphyronotum, a new species from Dafengding Nature Reserve, Sichuan Province, China, is proposed. Diagnostic morphological characters, full description and detailed illustration are given based on the type material. A comparison between this new species and the two most similar congeners are presented.

Data from: Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles

Yong-Fang Yao, Qiu-Xia Dai, Jing Li, Qing-Yong Ni, Ming-Wang Zhang & Huai-Liang Xu
Background: Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some...

Data from: Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

Xiao-Juan Wang, Quan-Jun Hu, Xin-Yi Guo, Kun Wang, Da-Fu Ru, Dmitry A. German, Elizabeth A. Weretilnyk, Richard J. Abbott, Martin Lascoux & Jian-Quan Liu
Eutrema salsugineum is a widely distributed species, which provide a good model to study long-distance dispersal and accumulation of deleterious mutations. Based on population genomic data, we clarified demographic history of E. salsugineum and showed how deleterious alleles accumulated.

Blow to the Northeast? Intraspecific differentiation of Populus davidiana suggests a northeastward skew of a phylogeographic break boundary in East Asia

Xiaoyan Fan, Xinya Song & Richard I. Milne
Aim: There is increasing interest in the role that biological traits, and historical and biogeographic processes, play in the formation of phylogeographic patterns. An arid belt that once existed in northern China might have affected many plants, but this has yet to be untested in an arid-tolerant, wind-dispersed species. Here we tested how intrinsic and extrinsic factors have affected the phylogeography of Populus davidiana. Location: East Asia Methods: Genetic variation was surveyed across 40 populations...

Data from: Fe3O4 nanoparticle coated mushroom source biomaterail for Cr(VI) polluted liquid treatment and mechanism research

Can Wang, Huakang Liu, Zizhao Liu, Yufeng Gao, Bin Wu & Heng Xu
Agrocybe cylindracea substrate-Fe3O4 (ACS-Fe3O4), a Fe3O4 nanoparticle coated biomaterial derived from agriculture waste from mushroom cultivating, was investigated to remove the hexavalent chromium ions (Cr(VI)) from aqueous solution. After modification, the material surface become uneven with polyporous and crinkly structure, improving the Cr-accommodation ability in a sound manner. Optimized by Taguchi method, Cr(VI) removal efficiency was up to 73.88% with 240min, 40°C, pH 3, Cr(VI) at 200 mg L-1, dosage at 12 g L-1, rpm...

Data from: Diploid hybrid origin of Ostryopsis intermedia (Betulaceae) in the Qinghai-Tibet Plateau triggered by Quaternary climate change

Bingbing Liu, Richard J. Abbott, Zhiqiang Lu, Bin Tian & Jianquan Liu
Despite the well known effects that Quaternary climate oscillations had on shaping intraspecific diversity, their role in driving homoploid hybrid speciation is less clear. Here we examine their importance in the putative homoploid hybrid origin and evolution of Ostryopsis intermedia, a diploid species occurring in the Qinghai-Tibet Plateau (QTP), a biodiversity hotspot. We investigated interspecific relationships between this species and its only other congeners, O. davidiana and O. nobilis, based on four sets of nuclear...

Data from: Taylor's Power Law and its decomposition in urban facilities

Liang Wu, Chi Gong & Xin Yan
As one of the few generalities in ecology, Taylor's power law admits a power function relationship $V=aM^{b}$ between the variance $V$ and mean number $M$ of organisms in a quadrat. We examine the spatial distribution data of seven urban service facilities in 37 major cities in China, and find that Taylor's law is validated among all types of facilities. Moreover, Taylor's law is robust if we shift the observation window or vary the size of...

Data from: A complex pattern of post-divergence expansion, contraction, introgression and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

Bin Tian, Yi Fu, Richard Milne, Kangshan Mao, Yong-Shuai Sun, Xiangguang Ma & Hang Sun
The well-known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry may postdate the species divergence. We examined this hypothesis using DNA sequence data from 3 chloroplast fragments and 5 nuclear loci of Dipelta floribunda and D. yunnanensis, two shrub species with the circum Sichuan Basin distribution, combining the climatic niche modeling approach. The best-fit model...

Data from: Agreements between industry and academia on publication rights: a retrospective study of protocols and publications of randomized clinical trials

Benjamin Kasenda, Erik Von Elm, John J. You, Anette Blümle, Yuki Tomonaga, Ramon Saccilotto, Alain Amstutz, Theresa Bengough, Joerg J. Meerpohl, Mihaela Stegert, Kelechi K. Olu, Kari A. O. Tikkinen, Ignacio Neumann, Alonso Carrasco-Labra, Markus Faulhaber, Sohail M. Mulla, Dominik Mertz, Elie A. Akl, Dirk Bassler, Jason W. Busse, Ignacio Ferreira-González, Francois Lamontagne, Alain Nordmann, Viktoria Gloy, Heike Raatz … & Matthias Briel
Background: Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications. We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees. Methods and Findings: We used a retrospective cohort of randomized clinical...

Preparation and regeneration of iron-modified nanofibres for low-concentration phosphorus-containing wastewater treatment

Ying Luo, Min Liu, Ying Chen, Tingting Wang & Wei Zhang
In this study, nanocellulose (CNFs) was prepared by a mechanical shearing method, a simple and pollution-free process. Iron hydroxide was loaded on nanocellulose, a natural macromolecule derived from bamboo, to produce the second generation iron-loaded nanocellulose for the removal of low-concentration phosphorus from wastewater. We found that the best modified ferric salt was ferric chloride. When the mass ratio of Fe(OH)3 and CNFs was 1.5:1, freeze-drying with liquid nitrogen yielded the best adsorption performance. The...

Data: Abiotic niche divergence of homoploid hybrid species from their progenitors

Danying Wang, Chen Shao, Yingying Zhu, Zhenxiang Xi, Xiaoting Xu & Jianquan Liu
Although more frequently reported recently than was previously expected, the role of ecology in the speciation of homoploid hybrid species (HHS) has not been quantitatively evaluated. We examined divergences in the niches of 22 assumed HHS (18 plants and four animals) from those of their progenitors using 52097 occurrences and 26 environmental factors (temperature, precipitation, altitude and soil). We identified three niche divergence patterns in HHS, niche novelty, niche contraction and niche intermediacy, by estimating...

The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

Liming Cai, Zhenxiang Xi, Emily Lemmon, Alan Lemmon, Austin Mast, Christopher Buddenhagen, Liang Liu & Charles Davis
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data...

Data from: The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

Qingqing Zhu, Lu Song, Guangdun Peng, Na Sun, Jun Chen, Ting Zhang, Nengyin Sheng, Wei Tang, Cheng Qian, Yunbo Qiao, Ke Tang, Jing-Dong Han, Jinsong Li, Naihe Jing & Jing-Dong Jackie Han
The neural fate commitment of pluripotent stem cells requires the repression of extrinsic inhibitory signals and the activation of intrinsic positive transcription factors. However, how these two events are integrated to ensure appropriate neural conversion remains unclear. Here, we showed that Pou3f1 is essential for the neural differentiation of mouse embryonic stem cells (ESCs), specifically during the transition from epiblast stem cells (EpiSCs) to neural progenitor cells (NPCs). Chimeric analysis showed that Pou3f1 knockdown leads...

Data from: Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species

Klaus-Peter Koepfli, John Pollinger, Raquel Godinho, Jacqueline Robinson, Amanda Lea, Sarah Hendricks, Rena M. Schweizer, Olaf Thalmann, Pedro Silva, Zhenxin Fan, Andrey A. Yurchenko, Pavel Dobrynin, Alexey Makunin, James A. Cahill, Beth Shapiro, Francisco Álvares, José C. Brito, Eli Geffen, Jennifer A. Leonard, Kristofer M. Helgen, Warren E. Johnson, Stephen J. O'Brien, Blaire Van Valkenburgh & Robert K. Wayne
The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a...

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: First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics

Lianming Du, Wujiao Li, Fujun Shen, Mingyu Yang, Zili Wang, Zhenxin Fan, Zuoyi Jian, Rong Hou, Bisong Yue & Xiuyue Zhang
The giant panda (Ailuropoda melanoleuca) is one of the most famous flagship species for conservation, and its draft genome has recently been assembled. However, the transcriptome is not yet available. In this study, the blood transcriptomes of three pandas were characterized and about 160 million sequencing reads were generated using Illumina HiSeq 2000 paired-end sequencing technology. The assembly yielded 92 598 transcripts with an average length of 1626 bp and N50 length of 2842 bp....

Data from: Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor

Xin Luo, Quanjun Hu, Pingping Zhou, Dan Zhang, Qian Wang, Richard J. Abbott, Yaling Wang & Jianquan Liu
Reconstructing the origin of a polyploid species is particularly challenging when an ancestor has become extinct. Under such circumstances, the extinct donor of a genome found in the polyploid may be treated as a ‘ghost’ species in that its prior existence is recognized through the presence of its genome in the polyploid. In this study, we aimed to determine the polyploid origin of Oxyria sinensis (2n = 40) for which only one congeneric species is...

Data from: Labor market integration of people with disabilities: results from the Swiss Spinal Cord Injury Cohort Study

Jan D. Reinhardt, Marcel W.M. Post, Christine Fekete, Bruno Trezzini, Martin W.G. Brinkhof, Marcel W. M. Post & Martin W. G. Brinkhof
Objectives: We aimed to describe labor market participation (LMP) of persons with spinal cord injury (SCI) in Switzerland, to examine potential determinants of LMP, and to compare LMP between SCI and the general population. Methods: We analyzed data from 1458 participants of employable age from the cross-sectional community survey of the Swiss Spinal Cord Injury Cohort Study. Data on LMP of the Swiss general population were obtained from the Swiss Federal Statistics Office. Factors associated...

Data from: Isaacs syndrome associated with GABAB and AChR antibodies in sarcomatoid carcinoma

Bi Zhao, Jingfang Lin, Xu Liu, Yan Zeng, Chunlan Jia, Weihua Guo, Xue Gong, Dong Zhou, Zhen Hong & Huifang Shang
Isaacs syndrome is an acquired peripheral nerve hyperexcitability syndrome characterized by twitching, painful cramps, stiffness, delayed muscle relaxation, and sweating.1 Needle EMG findings include continuous single motor unit discharges occurring as doublets, triplets, and multiplet single unit discharges firing at higher rates (150–300 Hz; neuromyotonic discharges) and at lower rates (less than 60 Hz; myokymic discharges).2 Isaacs syndrome has been reported in patients with thymoma, small-cell lung carcinoma (SCLC), or lymphoma.2 Antibodies specific for voltage-gated...

Data from: Phylogenetic conservatism and biogeographic affinity influence woody plant species richness-climate relationships in eastern Eurasia

Xiangyan Su, Nawal Shrestha, Xiaoting Xu, Denis Sandanov, Qinggang Wang, Siyang Wang, Dimitar Dimitrov & Zhiheng Wang
Mechanisms underlying species richness patterns remain a central yet controversial issue in biology. Climate has been regarded as a major determinant of species richness. However, the relative influences of different evolutionary processes, (i.e. niche conservatism, diversification rate, and time for speciation) on species richness-climate relationships remain to be tested. Here, using newly compiled distribution maps for 11,422 woody plant species in eastern Eurasia, we estimated species richness patterns for all species and for families with...

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