81 Works

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...

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...

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: 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...

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: 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: Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes

Langyu Gu & Canwei Xia
Background: Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. Results: Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the...

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: 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: 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: Environmental and evolutionary drivers of diversity patterns in the tea family (Theaceae s.s.) across China

Mide Rao, Manuel J. Steinbauer, Xiaoguo Xiang, Minggang Zhang, Xiangcheng Mi, Jin-Tun Zhang, Keping Ma, Jens-Christian Svenning & Jintun Zhang
Subtropical forest is recognized as an important global vegetation type with high levels of plant species richness. However, the mechanisms underlying its diversity remain poorly understood. Here, we assessed the roles of environmental drivers and evolutionary dynamics (time-for-speciation and diversification rate) in shaping species richness patterns across China for a major subtropical plant group, the tea family (Theaceae s.s.) (145 species), at several taxonomic scales. To this end, we assessed the relationships between species richness,...

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: 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...

Alterations ion channel expression in prefrontal cortex of a mouse model of schizophrenia

Zhen Mi & Yousheng Shu
Maternal immune activation (MIA) and juvenile social isolation (SI) are two most prevalent and widely accepted environmental insults that could increase the propensity of psychiatric illnesses. Using a two-hit model, we examined the impact of these two factors on expressions of voltage-gated sodium (Nav) and small conductance calcium-activated potassium (SK) channels in the prefrontal cortex (PFC). We found that MIA-SI significantly increased the expression level of Nav1.2 and SK3 channels that contribute to the somatodendritic...

Data from: A migratory divide spanning two continents is associated with genomic and ecological divergence

Sheela Turbek, Drew Schield, Elizabeth Scordato, Andrea Contina, Xin-Wei Da, Yang Liu, Yu Liu, Emilio Pagani-Núñez, Qing-Miao Ren, Chris Smith, Craig Stricker, Michael Wunder, David Zonana & Rebecca Safran
Migratory divides are contact zones between breeding populations with divergent migratory strategies during the non-breeding season. These locations provide an opportunity to evaluate the role of seasonal migration in the maintenance of reproductive isolation, particularly the relationship between population structure and features associated with distinct migratory strategies. We combine light-level geolocators, genomic sequencing, and stable isotopes to investigate the timing of migration and migratory routes of individuals breeding on either side of a migratory divide...

Data from: Evaluating staging habitat quality to advance the conservation of a declining migratory shorebird, Red Knot Calidris canutus

Tong Mu, Shangxiao Cai, Hebo Peng, Chris J. Hassell, Adrian Boyle, Zhengwang Zhang, Theunis Piersma & David Wilcove
Identifying where and when population “bottlenecks” occur is critical to the conservation of migratory species, many of which are declining precipitously worldwide. Especially challenging is the evaluation of changes to staging sites. These sites are indispensable links in the migratory cycle but are typically used only briefly. We devised a field-based approach to assess the quality and carrying capacity of a critical staging site in Nanpu, China, for the declining, migratory Red Knot (Calidris canutus...

Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years

Yi Hu, Catherine D’Amelio, Benoît Béchade, Christian Cabuslay, Piotr Lukasik, Jon Sanders, Shauna Price, Emily Fanwick, Scott Powell, Corrie Moreau & Jacob Russell
Sustaining beneficial gut symbioses presents a major challenge for animals, Including holometabolous insects. Social insects may meet such challenges through behavioral symbiont transfer and transgenerational inheritance through colony founders. We address such potential through colony-wide explorations across 13 eusocial, holometabolous ant species in the genus Cephalotes. Through amplicon sequencing and qPCR, we show that previously characterized worker microbiomes are largely conserved across adult castes, that adult microbiomes exhibit strong trends of phylosymbiosis, and that Cephalotes...

Data from: Phosphorus alleviation of nitrogen-suppressed methane sink in global grasslands

Lihua Zhang, Fenghui Yuan, Junhong Bai, Hongtao Duan, Xueying Gu, Longyu Hou, Yao Huang, Mingan Yang, Jinsheng He, Zhenghua Zhang, Lijun Yu, Changchun Song, David Lipson, Donatella Zona, Walter Oechel, Ivan Janssens & Xiaofeng Xu
Grassland ecosystems account for more than 10% of the global CH4 sink in soils. A 4-year field experiment found that addition of P alone did not affect CH4 uptake and experimental addition of N alone significantly suppressed CH4 uptake, while concurrent N and P additions suppressed CH4 uptake to a lesser degree. A meta-analysis including 382 data points in global grasslands corroborated these findings. Global extrapolation with an empirical modeling approach estimated that contemporary N...

Rivers as the largest source of mercury to coastal oceans worldwide

Maodian Liu, Qianru Zhang, Taylor Maavara, Shaoda Liu, Xuejun Wang & Peter Raymond
Mercury is a potent neurotoxic substance and accounts for 250,000 intellectual disabilities annually. Worldwide, coastal fisheries contribute the majority of human exposure to mercury through fish consumption. Recent global mercury cycling and risk models attribute all the mercury loading to the ocean to atmospheric deposition. Nevertheless, new regional research has noted that the riverine mercury export to coastal oceans may also be significant to the oceanic burden of mercury. Here we construct an unprecedented high-spatial-resolution...

Regionally divergent drivers of historical diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

Yang Liu, Simin Liu, Edouard Jelen, Mansour Alibadian, Cheng-Te Yao, Xintong Li, Nasrin Kayvanfar, Yutao Wang, Farhad Vahidi, Jianlin Han, Gombobaatar Sundev, Zhengwang Zhang & Manuel Schweizer
Aim: Pleistocene climate and associated environmental changes have influenced phylogeographic patterns of many species. These not only depend on a species’ life history but also vary regionally. Consequently, populations of widespread species that occur in several biomes might display different evolutionary trajectories. We aimed to identify regional drivers of diversification in the common pheasant, a widely distributed ecological generalist. Study location: Asia Taxon: Common pheasant Phasianus colchicus Methods: Using a comprehensive geographic sampling of 204...

The impact of urbanization on body size of Barn Swallows Hirundo rustica gutturalis

Yanyan Zhao, Yu Liu, Elizabeth Scordato, Myung-Bok Lee, Xiaoying Xing, Xinyuan Pan, Yang Liu, Rebecca Safran & Emilio Pagani-Núñez
Urbanization implies a dramatic impact on ecosystems, which may lead to drastic phenotypic differences between urban and non-urban individuals. For instance, urbanization is associated with increased metabolic costs, which may constrain body size, but urbanization also leads to habitat fragmentation, which may favour increases in body mass when for instance it correlates with dispersal capacity. However, this apparent contradiction has rarely been studied. This is particularly evident in China where the urbanization process is currently...

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: 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: 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...

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...

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