Topographic changes during the Pleistocene glacial/interglacial cycles affected the distribution of coastline mangroves and influenced their population genetic structure. The submergence of the continental shelf off southeast China during the postglacial age caused coastline expansions and resulted in the colonization of mangroves. Here, we performed multilocus genome scans using amplified fragment-length polymorphisms to explore the effects of topography and natural selection in structuring Kandelia obovata populations. Long-term isolation by the Taiwan Strait since the end...

An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programs that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world, yet the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, i.e., the common and flare cultivated tree peonies, was a single...

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...

Movements of individuals within and among populations help to maintain genetic variability and population viability. Therefore, understanding landscape connectivity is vital for effective species conservation. The snow leopard is endemic to mountainous areas of Central Asia and occurs within 12 countries. We assess potential connectivity across the species’ range to highlight corridors for dispersal and genetic flow between populations, prioritizing research and conservation action for this wide-ranging, endangered top-predator. We used resistant kernel modeling to...

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...

What confers invasive alien plants a competitive advantage over native plants remains open to debate. Many of the world's worst invasive alien plants are clonal and able to share resources within clones (clonal integration), particularly in heterogeneous environments. Here, we tested the hypothesis that clonal integration benefits invasive clonal plants more than natives and thus confers invasives a competitive advantage. We selected five congeneric and naturally co-occurring pairs of invasive alien and native clonal plants...

Long-lived tree species are genetically differentiated and locally adapted with respect to fitness-related traits, but the genetic basis of local adaptation remains largely unresolved. Recent advances in population genetics and landscape genomic analyses enable identification of putative adaptive loci and specific selective pressures acting on local adaptation. Here we sampled 60 evergreen oak (Quercus aquifolioides) populations throughout the species’ range and pool-sequenced 587 individuals at drought stress candidate genes. We analyzed patterns of genetic diversity...

Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar...

1. Changes in precipitation regimes and nitrogen deposition levels due to global change are altering terrestrial ecosystems worldwide. Most attempts at understanding how biotic interactions affect plant species and community responses to global change have focused on biotic interactions measured at the community-level. However, these approaches ignore that communities include functionally dissimilar species that might respond differently to changes in the effects of dominant neighbours along environmental gradients. We test the hypothesis that plant species...

By assessing the influence of rhizocompartment types (i.e. root, rhizosphere soil, root zone soil, and inter-shrub bulk soil) on the diversity of soil microbial communities under desert leguminous plant shrubs, and the influence of, and variations in, soil physicochemical factors in interactions among leguminous plants, soil, and microbes. Both 16S rRNA high-throughput genome sequencing and conventional soil physicochemical index determination were used to characterise the bacterial diversity and soil physicochemical properties in the rhizocompartments of...

The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability and phylogeography of 53 specimens of...

Replication-competent vesicular stomatitis virus (VSV)-based recombinant viruses are useful tools for studying emerging and highly pathogenic enveloped viruses in level 2 biosafety facilities. Here, we used a replication-competent recombinant VSVs (rVSVs) encoding the spike (S) protein of SARS-CoV-2 in place of the original G glycoprotein (rVSV-eGFP-SARS-CoV-2) to develop a high-throughput entry assay for SARS-CoV-2. The S protein was incorporated into the recovered rVSV-eGFP-SARS-CoV-2 particles, which could be neutralized by sera from convalescent COVID-19 patients. The...

This paper studies distributed estimation and inference for a general statistical problem with a convex loss that could be non-differentiable. For the purpose of efficient computation, we restrict ourselves to stochastic first-order optimization, which enjoys low per-iteration complexity. To motivate the proposed method, we first investigate the theoretical properties of a straightforward Divide-and-Conquer Stochastic Gradient Descent (DC-SGD) approach. Our theory shows that there is a restriction on the number of machines and this restriction becomes...

This article studies distributed estimation and inference for a general statistical problem with a convex loss that could be nondifferentiable. For the purpose of efficient computation, we restrict ourselves to stochastic first-order optimization, which enjoys low per-iteration complexity. To motivate the proposed method, we first investigate the theoretical properties of a straightforward divide-and-conquer stochastic gradient descent approach. Our theory shows that there is a restriction on the number of machines and this restriction becomes more...

Nitrogen (N), phosphorus (P), and acid deposition are co-occurring in many ecosystems, likely with complex interactive effects on litter decomposition. Few studies have been conducted to distinguish the interactive effects of these three factors on forest litter decomposition. Thus, we performed a 5-year litter decomposition experiment with N, P, acid addition in a temperate forest of Changbai Mountain in China, including four litter types from Pinus koraiensis, Quercus mongolica, Tilia amurensis and their mixtures. Our...

Geographical gradients in species diversity have long fascinated biogeographers and ecologists. However, the extent and generality of the positive/negative effects of the important factors governing functional diversity (FD) patterns are still debated, especially for the freshwater domain. We examined lake productivity and functional richness (FRic) of waterbirds sampled from 35 lakes and reservoirs in northern China with a geographic coverage of over 5 million km2. We used structural equation modelling (SEM) to explore the causal...

Natural plant-derived protein with excellent bioactivities has attracted much attention so a functional protein with molecular weight of 15.2 kDa was extracted from Millettia speciosa Champ. leaf for the first time. Under the pH of 12.0, solid-liquid ratio of 1:40 (w/v), extraction time of 2.0 h, and extraction temperature of 50 °C, the highest extracting efficiency (79.25 ± 0.78%) of the Millettia speciosa Champ. leaf protein (MLP) was achieved. The main structure of MLP contained...

The arthropod communities are influenced by both local conditions and features of the surrounding landscape. Landscape complexity and stand factors may both influence arthropod communities in poplar forests, but the multi-scale effects of these factors on poplar defoliators and natural enemies are still poorly understood. We collected poplar arthropods at 30 sampling sites within 5 forest landscapes in Xinjiang, China and assessed whether landscape complexity and stand factors influence species abundance and diversity of poplar...

1. Ectomycorrhizal (ECM) symbiosis is an evolutionary biological trait of higher plants for effective nutrient uptakes. However, little is known that how the formation and morphological differentiations of ECM roots mediate the nutrients of below- and aboveground plant tissues and the balance among nutrient elements across environmental gradients. Here we investigated the effects of ECM foraging strategies on root and foliar N and P concentrations and N:P ratio Abies faxoniana under variations of climate and...

The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence,...

The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence,...

The relationship between childbirth delivery methods and the risk of wheezing in children remains controversial. Few studies have explored it under different maternal conditions. To explore the influence of childbirth delivery method on the onset of wheezing in children of different parity. A total of 21716 patients were included in this retrospective observational study. Multivariable logistic regression was used to analyze the relationship between childbirth delivery method and wheezing in children under 18 years of...

Additional file 7: Figure S3. miRNAs with different expression patterns in crown and leaf tissues at the winter dormancy stage, spring green-up stage and jointing stage.

Additional file 2: Figure S1. Common and specific known miRNAs expressed in wheat crown tissues at four different growth and development stages.

Additional file 1: Table S1. Expression of known miRNAs identified in wheat crown tissues.