Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an “ancient” isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

Breeding semi-dwarf varieties to improve lodging resistance has been proven to be enormously successful in increasing grain yield since the advent of the "green revolution." However, the breeding of the majority of semi-dwarf rice varieties in Asia has been dependent mainly on genetic introduction of the mutant alleles of SD1, which encodes a gibberellin (GA) 20-oxidase, OsGA20ox2, for catalyzing GA biosynthesis. Here, we report a new rice lodging-resistance gene, Shortened Basal Internodes (SBI), which encodes a gibberellin 2-oxidase and specifically controls the elongation of culm basal internodes through deactivating GA activity. SBI is predominantly expressed in culm basal internodes. Genetic analyses indicate that SBI is a semi-dominant gene affecting rice height and lodging resistance. SBI allelic variants display different activities and are associated with the height of rice varieties. Breeding with higher activity of the SBI allele generates new rice varieties with improved lodging resistance and increased yield. The discovery of the SBI provides a desirable gene resource for producing semi-dwarf rice phenotypes and offers an effective strategy for breeding rice varieties with enhanced lodging resistance and high yield.

mir-548 is a larger, poorly conserved primate-specific miRNA gene family. 69 human mir-548 genes located in almost all human chromosomes whose widespread distribution pattern implicates the evolutionary origin from transposable elements. Higher level of nucleotide divergence was detected between these human miRNA genes, which mainly derived from divergence of multicopy pre-miRNAs and homologous miRNA genes. Products of  mir-548, miR-548-5p, and miR-548-3p showed inconsistent evolutionary patterns, which partly contributed to larger genetic distances between pre-miRNAs. “Seed shifting” events could be detected among miR-548 sequences due to various 5′ ends. The events led to shift of seed sequences and target mRNAs, even generated to new target mRNAs. Additionally, the phenomenon of miRNA:miRNA interaction in the miRNA gene family was found. The potential interaction between miRNAs may be contributed to dynamic miRNA expression profiles by complementarily binding events to form miRNA:miRNA duplex with 5′-/3′-overhangs. The miRNA gene family had important roles in multiple biological processes, including signaling pathways and some cancers. The potential abundant roles and functional implication further led to the larger and poorly conserved gene family with genetic variation based on transposable elements. The evolutionary pattern of the primate-specific gene family might contribute to dynamic expression profiles and regulatory network.

Although the World Wide Web has opened the door for businesses and consumers across the globe, many issues and challenges remain in order to take full advantage of this unprecedented opportunity. More specifically, businesses engaged in electronic commerce can take advantage of current technologies that allow them to collect vast amounts of information about their customers. Although many companies use this information to tailor products and services to improve their relationship with their customers, many people simply do not trust most organizations that require the exchange of personal information. Recent studies suggest that many people either decline to provide this information over the Internet or simply provide false information. As electronic commerce companies extend their reach globally, the issues concerning privacy and trust must be extended beyond a single national culture. This study proposes and tests a Privacy-Trust-Behavioral Intention Model from a global perspective. More specifically, this study compares American and Taiwanese perceptions concerning online privacy and how it relates to the level of trust with a company’s electronic commerce web site. In turn, the model suggests that trust is an important intermediary variable that influences behavioral intentions for online transactions.

NPHIs can be fatal but they can be managed with satisfactory results by proper preoperative imaging evaluation, rapid appropriate surgical management, and accurate postoperative care. Personalized surgical intervention should be undertaken depending on the mechanism and extent of the NPHI.

Our goal in developing the MultiWaver software series was to be able to infer population admixture history under various complex scenarios. The earlier version of MultiWaver considered only discrete admixture models. Here, we report a newly developed version, MultiWaver 2.0, that implements a more flexible framework and is capable of inferring multiple-wave admixture histories under both discrete and continuous admixture models. MultiWaver 2.0 can automatically select an optimal admixture model based on the length distribution of ancestral tracks of chromosomes, and the program can estimate the corresponding parameters under the selected model. Specifically, for discrete admixture models, we used a likelihood ratio test (LRT) to determine the optimal discrete model and an expectation-maximization algorithm to estimate the parameters. In addition, according to the principles of the Bayesian Information Criterion (BIC), we compared the optimal discrete model with several continuous admixture models. In MultiWaver 2.0, we also applied a bootstrapping technique to provide levels of support for the chosen model and the confidence interval (CI) of the estimations of admixture time. Simulation studies validated the reliability and effectiveness of our method. Finally, the program performed well when applied to real datasets of typical admixed populations, such as African Americans, Uyghurs, and Hazaras.

With laminectomy being widely accepted as the treatment for lumbar disorders, epidural fibrosis (EF) is a common complication for both the patients and the surgeons alike. Currently, EF is thought to cause recurrent postoperative pain after laminectomy or after discectomy. Angelica sinensis is a traditional Chinese medicine which has shown anti-inflammatory, antifibrotic, and antiproliferative properties. The object of this study was to investigate the effects of Angelica sinensis on the prevention of post-laminectomy EF formation in a rat model. A controlled double-blinded study was conducted in sixty healthy adult Wistar rats that underwent laminectomy at the L1-L2 levels. They were divided randomly into 3 groups according to the treatment method, with 20 in each group: (1) Angelica sinensis treatment group, (2) saline treatment group, and (3) sham group (laminectomy without treatment). All rats were euthanized humanely 4 weeks after laminectomy. The hydroxyproline content, Rydell score, vimentin cells density, fibroblasts density, inflammatory cells density, and inflammatory factors expressions all suggested better results in Angelica sinensis group than the other two groups. Topical application of Angelica sinensis could inhibit fibroblasts proliferation and TGF-β1 and IL-6 expressions and prevent epidural scar adhesion in postlaminectomy rat model.