86 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: 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...

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: 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: 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: 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...

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...

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...

Do annual and perennial populations of an insect-pollinated plant species differ in mating system?

Wei-Ning Bai, Yue Ma, Spencer Barrett, Fang-Yuan Wang & Jun-Chen Deng
Background and Aims Theory predicts that outcrossing should be more prevalent among perennials than annuals, a pattern confirmed by comparative evidence from diverse angiosperm families. However, intraspecific comparisons between annual and perennial populations are few because such variation is uncommon among flowering plants. Here, we test the hypothesis that perennial populations outcross more than annual populations by investigating Incarvillea sinensis, a wide-ranging insect-pollinated herb native to China. The occurrence of both allopatric and sympatric populations...

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...

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...

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