25 Works

Data from: Mitochondrial genomes of domestic animals need scrutiny

Ni-Ni Shi, Long Fan, Yong-Gang Yao, Min-Sheng Peng & Ya-Ping Zhang
More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives, as well. Nevertheless, few efforts have been performed to evaluate the sequence data quality. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that...

Data from: The first flea with fully distended abdomen from the Early Cretaceous of China

Taiping Gao, Chungkun Shih, Alexandr P. Rasnitsyn, Xing Xu, Shuo Wang & Dong Ren
Background: Fleas, the most notorious insect ectoparasites of human, dogs, cats, birds, etc., have recently been traced to its basal and primitive ancestors during the Middle Jurassic. Compared with extant fleas, these large basal fleas have many different features. Although several fossil species with transitional morphologies filled the evolutionary blank, the early evolution of these ectoparasites is still poorly known. Results: Here we report a new flea with transitional morphology, Pseudopulex tanlan sp. nov., assigned...

Data from: Comparative phylogeography of the plateau zokor (Eospalax baileyi) and its host-associated flea (Neopsylla paranoma) in the Qinghai-Tibet Plateau

Gonghua Lin, Fang Zhao, Hongjian Chen, Xiaogong Deng, Jianping Su & Tongzuo Zhang
Background: Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite’s phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared the population genetics of the plateau zokor (Eospalax baileyi), a subterranean rodent, and its host-associated flea species, Neopsylla paranoma, with an aim to determine whether the two animals share a similar phylogeographic pattern....

Data from: Nitrogen saturation in humid tropical forests after 6 years of nitrogen and phosphorus addition: hypothesis testing

Hao Chen, Geshere A. Gurmesa, Wei Zhang, Xiaomin Zhu, Mianhai Zheng, Qinggong Mao, Tao Zhang & Jiangming Mo
Nitrogen (N) saturation hypothesis suggests that when an ecosystem reaches N-saturation, continued N input will cause increased N leaching, nitrous oxide (N2O) emission, and N mineralization and nitrification rates. It also suggests that a different element will become the main limiting factor when N saturation has been reached. Although this hypothesis has been tested in temperate forests, whether they can be directly applied to N-saturated tropical forests remain poorly addressed. To test this hypothesis, soil...

Data from: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?

Zuo-Dong Wei, Noppol Kobmoo, Astrid Cruaud, Finn Kjellberg & Z.-D. Wei
Obligate mutualistic nursery pollination systems between insects and plants have led to substantial co-diversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases host plants sharing pollinators are allopatric. However in the case of the species...

Data from: Phylogeography and evolution of a fungal-insect association on the Tibetan Plateau

Yongjie Zhang, Shu Zhang, Yuling Li, Shaoli Ma, Chengshu Wang, Meichun Xiang, Xin Liu, Zhiqiang An, Jianping Xu & Xingzhong Liu
Parasitoidism refers to a major form of inter-species interactions where parasitoids sterilize and/or kill their hosts typically before hosts reach reproductive age. However, relatively little is known about the evolutionary dynamics of parasitoidism. Here we investigate the spatial patterns of genetic variation of Chinese cordyceps, including both the parasitoidal fungus Ophiocordyceps sinensis and its host insects. We sampled broadly from alpine regions on the Tibetan Plateau and obtained sequences on seven fungal and three insect...

Data from: Phantom alternatives influence food preferences in the eastern honey bee Apis cerana

Ken Tan, Shihao Dong, Xiwen Liu, Weiweng Chen, Yuchong Wang, Benjamin P. Oldroyd & Tanya Latty
1. Most models of animal choice behaviour assume that desirable but unavailable options, such as a high quality, but inhabited nest site, do not influence an individual’s preferences for the remaining options. However, experiments suggest that in mammals such ‘phantom’ alternatives can alter, and even reverse, an individual’s preferences for other items in a choice set. 2. Here we investigate the effect of phantom alternatives on feeder preferences in the eastern honey bee, Apis cerana....

Data from: Multi-locus phylogeny of lethal amanitas: implications for species diversity and historical biogeography

Qing Cai, Rodham E. Tulloss, Li P. Tang, Bau Tolgor, Ping Zhang, Zuo H. Chen & Zhu L. Yang
Background: Lethal amanitas (Amanita section Phalloideae) are a group of wild, fatal mushrooms causing many poisoning cases worldwide. However, the diversity and evolutionary history of these lethal mushrooms remain poorly known due to the limited sampling and insufficient gene fragments employed for phylogenetic analyses. In this study, five gene loci (nrLSU, ITS, rpb2, ef1-α and β-tubulin) with a widely geographic sampling from East and South Asia, Europe, North and Central America, South Africa and Australia...

Data from: Introduction beyond a species range: a relationship between population origin, adaptive potential and plant performance

Sergei Volis, Danara Ormanbekova, Kanat Yermekbayev, Minshu Song & Irina Shulgina
The adaptive potential of a population defines its importance for species survival in changing environmental conditions such as global climate change. Very few empirical studies have examined adaptive potential across species’ ranges, namely, of edge vs core populations, and we are unaware of a study that has tested adaptive potential (namely, variation in adaptive traits) and measured performance of such populations in conditions not currently experienced by the species but expected in the future. Here...

Data from: \"Transcriptome resources for the marmot flea and plague vector, Oropsylla silantiewi\" in Genomic Resources Notes accepted 1 February 2014 to 31 March 2014

Gonghua Lin, Zuyun Wang, Michael F. Whiting, Jianping Su, Fang Zhao, Junying Ma, Hongjian Chen & Tongzuo Zhang
This article documents the public availability of raw transcriptome sequence data, 47,882 assembled unigenes as well as their functional annotations, and 13,052 deduced ORFs (open reading frame) of a plague vector Oropsylla silantiewi.

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: Deep phylogenetic incongruence in the angiosperm clade Rosidae

Miao Sun, Douglas E. Soltis, Pamela S. Soltis, Xinyu Zhu, J. Gordon Burleigh & Zhiduan Chen
Analysis of large data sets can help resolve difficult nodes in the tree of life and also reveal complex evolutionary histories. The placement of the Celastrales-Oxalidales-Malpighiales (COM) clade within Rosidae remains one of the most confounding phylogenetic questions in angiosperms, with previous analyses placing it with either Fabidae or Malvidae. To elucidate the position of COM, we assembled multi-gene matrices of chloroplast, mitochondrial, and nuclear sequences, as well as large single- and multi-copy nuclear gene...

Data from: Development of genomic resources for Nothofagus species using next-generation sequencing data

Veronica Andrea El Mujtar, Leonardo Ariel Gallo, Lang Tiange & Pauline Garnier-Gere
Using next-generation sequencing, we developed the first whole-genome resources for two hybridizing Nothofagus species of the Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimization of the putative chloroplast gene map yielded ~32 000 contigs from 43% of the reads produced. With 12.5% of assembled reads, we covered ~96% of the chloroplast genome and ~70% of the mitochondrial gene content,...

Data from: Discovery of a relict lineage and monotypic family of passerine birds

Per Alström, Daniel M. Hooper, Yang Liu, Urban Olsson, Dhananjai Mohan, Magnus Gelang, Hung Le Manh, Jian Zhao, Fumin Lei, Trevor D. Price & P. Alstrom
Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the ‘bombycillids’ (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and...

Data from: Cross-cultural variation in men’s preference for sexual dimorphism in women’s faces

Mikhail V. Kozlov, Huajian Cai, Jorge Contreras-Garduño, Barnaby J. Dixson, Gavita A. Oana, Gwenaël Kaminski, Norman P. Li, Minna T. Lyons, Ike E. Onyishi, Keshav Prasai, Farid Pazhoohi, Pavol Prokop, Sandra L. Rosales Cardozo, Nicolle Sydney, Jose C. Yong, Markus J. Rantala, U. M. Marcinkowska & J. Contreras-Garduno
Both attractiveness judgements and mate preferences vary considerably cross-culturally. We investigated whether men's preference for femininity in women's faces varies between 28 countries with diverse health conditions by analysing responses of 1972 heterosexual participants. Although men in all countries preferred feminized over masculinized female faces, we found substantial differences between countries in the magnitude of men's preferences. Using an average femininity preference for each country, we found men's facial femininity preferences correlated positively with the...

Data from: Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

Li-Na Zhang, Xian-Zhi Zhang, Yu-Xiao Zhang, Chun-Xia Zeng, Peng-Fei Ma, Lei Zhao, Zhen-Hua Guo & De-Zhu Li
The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared to...

Data from: Long-term balanced fertilization improves the soil microbial functional diversity in a phosphorus-limited paddy soil

Jian-Qiang Su, Long-Jun Ding, Kai Xue, Huai-Ying Yao, John Quensen, Shi-Jie Bai, Wen-Xue Wei, Jin-Shui Wu, Jizhong Zhou, James M. Tiedje & Yong-Guan Zhu
The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, GeoChip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control...

Data from: Comparative transcriptome resources of eleven Primulina species, a group of “stone plants” from a biodiversity hotspot

Bin Ai, Yong Gao, Xiaolong Zhang, Junjie Tao, Ming Kang & Hongwen Huang
The genus Primulina is an emerging model system in studying the drivers and mechanisms of species diversification, for its high species richness and endemism, together with high degree of habitat specialization. In this study, we sequenced transcriptomes for eleven Primulina species across the phylogeny of the genus using the Illumina HiSeq 2000 platform. A total of 336 million clean reads were processed into 355 573 unigenes with a mean length of 1336 bp and an...

Data from: Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

Gong-Hua Lin, Kun Wang, Xiao-Gong Deng, Eviatar Nevo, Fang Zhao, Jian-Ping Su, Song-Chang Guo, Tong-Zuo Zhang & Huabin Zhao
Background: Subterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground, however, the scarcity of genomic information limits our better understanding of their evolutionary history. Owing to the convergence of morphological traits and the incongruence of molecular data, the phylogenetic relationships among three subfamilies Myospalacinae (zokors), Spalacinae (blind mole rats) and Rhizomyinae (bamboo rats) within the family Spalacidae remain unresolved. Here, we performed de novo...

Data from: Maternal effects and population regulation: maternal density-induced reproduction suppression impairs offspring capacity in response to immediate environment in root voles Microtus oeconomus

Jiang-Hui Bian, Shou-Yang Du, Yan Wu, Yi-Fan Cao, Xu-Heng Nie, Hui He & Zhi-Bing You
1. The hypothesis that maternal effects act as an adaptive bridge in translating maternal environments into offspring phenotypes and thereby affecting population dynamics has not been studied in the well-controlled fields. 2. In this study, the effects of maternal population-density on offspring stress axis, reproduction and population dynamics were studied in root voles (Microtus oeconomus). Parental enclosures for breeding offspring were established by introducing 6 adults per sex into each of 4 (low density) and...

Data from: Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers

Jin Pan, Baosheng Wang, Zhi-Yong Pei, Wei Zhao, Jie Gao, Jian-Feng Mao & Xiao-Ru Wang
Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing...

Data from: The incidence and pattern of co-pollinator diversification in dioecious and monoecious figs

Li Yuan Yang, Carlos A. Machado, Xiao-Dong Dang, Yan-Qiong Peng, Da-Rong Yang, Wan-Jin Liao, Da-Yong Zhang & Li-Yuan Yang
Differences in breeding system are associated with correlated ecological and morphological changes in plants. In Ficus, dioecy and monoecy are strongly associated with different suites of traits (tree height, population density, fruiting frequency, pollinator dispersal ecology). Although ~30% of fig species are pollinated by multiple species of fig-pollinating wasps it has been suggested that co-pollinators are rare in dioecious figs. Here we test whether there is a connection between fig breeding system and co-pollinator incidence...

Data from: Leaf P increase outpaces leaf N in an Inner Mongolia grassland over 27 years

Zhaorong Mi, Yuanyuan Huang, Huijie Gan, Wenjia Zhou, Dan F. B. Flynn, Jin-Sheng He & J.-S. He
The dynamics of leaf nitrogen (N) and phosphorus (P) have been intensively explored in short-term experiments, but rarely at longer timescales. Here, we investigated leaf N : P stoichiometry over a 27-year interval in an Inner Mongolia grassland by comparing leaf N : P concentration of 2006 with that of 1979. Across 80 species, both leaf N and P increased, but the increase in leaf N lagged behind that of leaf P, leading to a...

Data from: Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (Poaceae)

Peng-Fei Ma, Yu-Xiao Zhang, Chun-Xia Zeng, Zhen-Hua Guo & De-Zhu Li
The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing 8 major lineages of Arundinarieae...

Data from: Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot

Zhuan Hao, Yuanwen Kuang & Ming Kang
1. Plant elemental properties are fundamentally important for physiology and biogeochemical cycling in ecosystems. No study has examined foliar elements and their interaction with soil and climate conditions at large geographic scales in Karst areas of China, a biodiversity hotspot in the world. Yet such information is important for understanding the functional diversity of nutrient strategies and the physiological adaptations of plants to climatic and edaphic heterogeneity. 2. We assessed the influence of phylogeny, soil...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Chinese Academy of Sciences
  • University of Chinese Academy of Sciences
  • Yunnan University
  • Institute of Subtropical Agriculture
  • Qinghai Institute for Endemic Diease Prevention and Control
  • Capital Normal University
  • Sun Yat-sen University
  • Institute of Plant Biology and Biotechnology
  • Chinese University of Hong Kong
  • Sichuan University