59 Works

Data from: Online spatial normalization for real-time fMRI

Xiaofei Li, Li Yao, Qing Ye & Xiaojie Zhao
Real-time functional magnetic resonance imaging (rtfMRI) is a recently emerged technique that demands fast data processing within a single repetition time (TR), such as a TR of 2 seconds. Data preprocessing in rtfMRI has rarely involved spatial normalization, which can not be accomplished in a short time period. However, spatial normalization may be critical for accurate functional localization in a stereotactic space and is an essential procedure for some emerging applications of rtfMRI. In this...

Data from: Donald’s ideotype and growth redundancy: a pot experimental test using an old and a modern spring wheat cultivar

Li Zhu & Da-Yong Zhang
Human selection for high crop yield under water-limited conditions should have led modern cereal cultivars to invest less in root biomass, be it unconsciously. To test this hypothesis we conducted a pot experiment with two spring wheat cultivars, one old and one modern, both widely grown in the semi-arid regions of China. Using the replacement series method introduced by de Wit, we showed that the older landrace (Monkhead) was significantly more competitive than the more-modern...

Data from: Phylogeographical patterns of an alpine plant, Rhodiola dumulosa (Crassulaceae), inferred from chloroplast DNA sequences

Yan Hou & Anru Lou
The phylogeographical patterns of Rhodiola dumulosa, an alpine plant species restrictedly growing in the crevices of rock piles, were investigated based on 4 fragments of the chloroplast genome. To cover the full distribution of R. dumulosa in China, 19 populations from 3 major disjunct distribution areas (northern, central, and northwestern China) were sampled. A total of 5881bp (after alignment) of chloroplast DNA (cpDNA) from 100 individuals were sequenced. The combined cpDNA data set yielded 36...

Undersampling correction methods to control γ-dependence for comparing β-diversity between regions

Ke Cao, Jens-Christian Svenning, Chuan Yan, Jintun Zhang, Xiangcheng Mi & Keping Ma
Measures of β-diversity are known to be highly constrained by the variation in γ-diversity across regions (i.e., γ-dependence), making it challenging to infer underlying ecological processes. Undersampling correction methods have attempted to estimate the actual β-diversity in order to minimize the effects of γ-dependence arising from the problem of incomplete sampling. However, no study has systematically tested their effectiveness in removing γ-dependence, and examined how well undersampling-corrected β-metrics reflect true β-diversity patterns that respond to...

Data from: Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation

Dong-Hao Zhou & Quan-Guo Zhang
Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbour very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment; and then imposed a one-individual-size population bottleneck on those surviving the antibiotic...

Assessing mammal species richness and occupancy in a Northeast Asian temperate forest shared by cattle

Jiawei Feng, Yifei Sun, Hailong Li, Yuqi Xiao, Dandan Zhang, James Smith, Jianping Ge & Tianming Wang
Aim: Asian forests are becoming increasingly degraded and fragmented by the extensive intensification of anthropogenic activities; these activities threaten wildlife and ecosystem sustainability. Facing a defaunation crisis, managers need more information on species assemblages to guide conservation efforts. We tested the relative influence of natural and anthropogenic factors on mammalian species richness and occupancy in temperate forests in Northeast Asia. Location: Northeast China. Methods: Camera-trapping data and multi-species occupancy models were used to estimate the...

Data from: Stability of a coevolving host-parasite system peaks at intermediate productivity

Xin-Feng Zhao, Yi-Qi Hao & Quan-Guo Zhang
Habitat productivity may affect the stability of consumer-resource systems, through both ecological and evolutionary mechanisms. We hypothesize that coevolving consumer-resource systems show more stable dynamics at intermediate resource availability, while very low-level resource supply cannot support sufficiently large populations of resource and consumer species to avoid stochastic extinction, and extremely resource-rich environments may promote escalatory arms-race-like coevolution that can cause strong fluctuations in species abundance and even extinction of one or both trophic levels.We tested...

Data from: Context-dependent strategies of food allocation among offspring in a facultative cooperative breeder

Jianqiang Li, Yong Wang, Lei Lv, Pengcheng Wang, Ben J. Hatchwell & Zhengwang Zhang
Natural selection should favor adoption of parental strategies that maximize fitness when allocating investment among offspring. In birds, begging displays often convey information of nestling need and quality, allowing parents to make adaptive food allocation decisions. We investigated how adults utilized cues likely to represent nestling competitive ability (begging position) and need (begging intensity), and a cue independent of nestling control (nestling sex) to distribute food among nestlings in a facultative cooperative breeder, the black-throated...

Data from: Phylogeography of Silver Pheasant (Lophura nycthemera L.) across China: aggregate effects of refugia, introgression and riverine barriers

Lu Dong, Gerald Heckel, Wei Liang & Yanyun Zhang
The role of Pleistocene glacial cycles in forming the contemporary genetic structure of organisms has been well studied in China with a particular focus on the Tibetan Plateau. However, China has a complex topography and diversity of local climates, and how glacial cycles may have shaped the subtropical and tropical biota of the region remains mostly unaddressed. To investigate the factors that affected the phylogeography and population history of a widely distributed and nondeciduous forest...

Data from: Genetic uniformity characterizes the invasive spread of water hyacinth (Eichhornia crassipes), a clonal aquatic plant

Yuan-Ye Zhang, Da-Yong Zhang & Spencer C.H. Barrett
Aquatic plant invasions are often associated with long-distance dispersal of vegetative propagules and prolific clonal reproduction. These reproductive features combined with genetic bottlenecks have the potential to severely limit genetic diversity in invasive populations. To investigate this question we conducted a global scale population genetic survey using Amplified Fragment Length Polymorphism (AFLP) markers of the world’s most successful aquatic plant invader – Eichhornia crassipes (water hyacinth). We sampled 1140 ramets from 54 populations from the...

Data from: Community-wide changes in inter-taxonomic temporal co-occurrence resulting from phenological shifts

Fangyuan Hua, Junhua Hu, Yang Liu, Xingli Giam, Tien Ming Lee, Hao Luo, Jia Wu, Qiaoyi Liang, Jian Zhao, Xiaoyan Long, Hong Pang, Biao Wang, Wei Liang, Zhengwang Zhang, Xuejie Gao & Jiang Zhu
Global climate change is known to affect the assembly of ecological communities by altering species’ spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species’ temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon...

Data from: Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai–Tibetan Plateau in a predatory bird

Shengkai Pan, Tongzuo Zhang, Zhengqin Rong, Li Hu, Zhongru Gu, Qi Wu, Shanshan Dong, Qiong Liu, Zhenzhen Lin, Lucia Deutschova, Xin-Hai Li, Andrew Dixon, Michael W. Bruford, Xiangjiang Zhan & Xinhai Li
Low oxygen and temperature pose key physiological challenges for endotherms living on the Qinghai–Tibetan Plateau (QTP). Molecular adaptations to high-altitude living have been detected in the genomes of Tibetans, their domesticated animals and a few wild species, but the contribution of transcriptional variation to altitudinal adaptation remains to be determined. Here we studied a top QTP predator, the saker falcon, and analysed how the transcriptome has become modified to cope with the stresses of hypoxia...

Regrowth strategies of Leymus chinensis in response to different grazing intensities

Zihe Zhang, Jirui Gong, Biao Wang, Xiaobing Li, Yong Ding, Bo Yang, Chenchen Zhu, Wei Zhang & Min Liu
In temperate grassland ecosystems, grazing can affect plant growth by foraging, trampling and excretion. The ability of dominant plant species to regrow after grazing is critical, since it allows the regeneration of photosynthetic tissues to support growth. We conducted a field experiment to evaluate the effects of different grazing intensities (control, light, medium, and heavy) on the physiological and biochemical responses of Leymus chinensis and the carbon (C) sources utilized during regrowth. Light grazing promoted...

Burrow ambient temperature influences Helice crab activity and availability for migratory Red-crowned Cranes Grus japonensis

Donglai Li, Jing Zhang, Lingyu Chen, Huw Lloyd & Zhengwang Zhang
For migratory birds that specialize on particular benthic macroinvertebrate species, the timing of migration is critical since prey availability may be temporally limited and a function of local ambient temperature. Hence, variation in local ambient temperature can influence the diet composition of migrant birds, and consequently they may be constrained by which stopover and wintering sites they are able to utilize during periods of colder temperatures. Here we use faecal analysis, observer-based population counts, digital...

Decreasing effects of precipitation on grassland spring phenology in temperate China

Xuancheng Zhou, Yongshuo Fu, Yaru Zhang, Xiaojun Geng, Fanghua Hao, Xuan Zhang, Heikki Hanninen, Yahui Guo & Hans J. De Boeck
Vegetation phenology is highly sensitive to climate change. The timing of spring phenology in temperate grasslands is primarily regulated by temperature and precipitation. This study aims to study whether the primary factor regulating vegetation phenology changed under ongoing climate change and its underlying mechanisms. In this study, we extracted Start of Season (SOS) dates using five standard methods from satellite-derived Normalized Difference Vegetation Index (NDVI) data and determined the primary regulating factor for spring phenology...

Data from: Disturbance and predation risk influence vigilance synchrony of Black-necked Cranes Grus nigricollis, but not as strongly as expected

Dejun Kong, Anders Pape Møller & Yanyun Zhang
Animals monitor surrounding dangers independently or cooperatively (synchronized and coordinated vigilance), with independent and synchronized scanning being prevalent. Coordinated vigilance, including unique sentinel behaviour, is rare in nature, since it is time-consuming and limited in terms of benefits. No evidence showed animals adopt alternative vigilance strategies during antipredation scanning yet. Considering the non-independent nature of both synchronization and coordination, we assessed whether group members could keep alert synchronously or in a coordinated fashion under different...

Energetic constraints imposed on trophic interaction strengths enhance resilience in empirical and model food webs

Xiaoxiao Li, Wei Yang, Ursula Gaedke & Peter De Ruiter
1. Food web stability and resilience are at the heart of understanding the structure and functioning of ecosystems. Previous studies show that models of empirical food webs are substantially more stable than random ones, due to a few strong interactions embedded in a majority of weak interactions. Analyses of trophic interaction loops show that in empirical food webs the patterns in the interaction strengths prevent the occurrence of destabilizing heavy loops and thereby enhances resilience....

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...

SSR genotypes and geographical locations of collections of three Asian butternuts and two species of Quercus

Yu Cao, Da-Yong Zhang, Wei-Ning Bai & Yan-Fei Zeng
In the file, we display the genotypes of 502 adult individuals of 17 natural Q. mongolica populations (QM), 139 individuals of 5 populations of northeast Q. liaotungensis (QL_ CBS), 240 individuals from 8 populations of northwest Q. liaotungensis (QL_ NWC), 596 individuals in 25 J. cathayensis (JC) populations, 399 individuals in 14 J. mandshurica populations (JM) and 107 individuals in 5 J. ailantifolia populations (JA). In addition, the sample information: geographical locations of collections and...

Data from: Identification of species in the angiosperm family Apiaceae using DNA barcodes

Jinxin Liu, Linchun Shi, Jianping Han, Geng Li, Heng Lu, Fanyun Meng, Stephen R. Downie, Jingyi Hou & Xiaoteng Zhou
Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The...

Data from: Simultaneous declines in summer survival of three shorebird species signals a flyway at risk

Theunis Piersma, Tamar Lok, Ying Chen, Chris J. Hassell, Hong-Yan Yang, Adrian Boyle, Matt Slaymaker, Ying-Chi Chan, David S. Melville, Zheng-Wang Zhang & Zhijun Ma
There is increasing concern about the world's animal migrations. With many land-use and climatological changes occurring simultaneously, pinning down the causes of large-scale conservation problems requires sophisticated and data-intensive approaches. Declining shorebird numbers along the East Asian–Australasian Flyway, in combination with data on habitat loss along the Yellow Sea (where these birds refuel during long-distance migrations), indicate a flyway under threat. If habitat loss at staging areas indeed leads to flyway-wide bird losses, we would...

Data from: Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

Yan-Fei Zeng, Wen-Ting Wang, Wan-Jin Liao, Hong-Fang Wang & Da-Yong Zhang
In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool-temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast...

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: Natural enemies govern ecosystem resilience in the face of extreme droughts

Qiang He, Brian Silliman, Zezheng Liu, Baoshan Cui & Brian R. Silliman
Severe droughts are on the rise in many regions. But thus far, attempts to predict when drought will cause a major regime shift or when ecosystems are resilient, often using plant drought tolerance models, have been frustrated. Here we show that pressure from natural enemies regulates an ecosystem’s resilience to severe droughts. Field experiments revealed that in protected salt marshes experiencing a severe drought, planting-eating grazers eliminated drought-stressed vegetation that could otherwise survive and recover...

Data from: Migration highways and migration barriers created by host-parasite interactions

Quan-Guo Zhang & Angus Buckling
Coevolving parasites may play a key role in host migration and population structure. Using coevolving bacteria and viruses, we test general hypotheses as to how coevolving parasites affect the success of passive host migration between habitats that can support different intensities of host-parasite interactions. First, we show that parasites aid migration from areas of intense to weak coevolutionary interactions and impede migration in the opposite direction, as a result of intraspecific apparent competition mediated via...

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