Browsing by Author "Wang, Wei"
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- Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plantsPublication . Xue, Jia-Yu; Dong, Shan-Shan; Wang, Ming-Qiang; Song, Tian-Qiang; Zhou, Guang-Can; Li, Zhen; Van de Peer, Yves; Shao, Zhu-Qing; Wang, Wei; Chen, Min; Zhang, Yan-Mei; Sun, Xiao-Qin; Chen, Hong-Feng; Zhang, Yong-Xia; Zhang, Shou-Zhou; Chen, Fei; Zhang, Liang-Sheng; Cox, Cymon; Liu, Yang; Wang, Qiang; Hang, Yue-YuThe early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon-sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony-informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.
- Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)Publication . Lu, Limin; Cox, C. J.; Mathews, Sarah; Wang, Wei; Wen, Jun; Chen, ZhiduanEvolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships of Vitaceae were retrieved by comprehensive comparisons of results from optimal partitioning analyses, multispecies coalescent approaches and the Bayesian concordance method. We found that partitioning schemes selected by PartitionFinder were preferred over those by gene or by codon position, and the unpartitioned model usually performed the worst. For a data set with conflicting signals, however, the unpartitioned model outperformed models that included more partitions, demonstrating some limitations to the effectiveness of concatenation for these data. For a transcriptome data set, fast coalescent methods (STAR and MP-EST) and a Bayesian concordance approach yielded congruent topologies with trees from the concatenated analyses and previous studies. Our results highlight that well-resolved gene trees are critical for the effectiveness of coalescent-based methods. Future efforts to improve the accuracy of phylogenomic analyses should emphasize the development of newmethods that can accommodate multiple biological processes and tolerate missing data while remaining computationally tractable. (C) The Willi Hennig Society 2017.
- Risk to patient safety from laboratory errors and delaysPublication . Wang, Wei; Alvarez, Luisa; Cavaco, IsabelIn most of the cases, patients are diagnosed and treated directly based on the clinical laboratory results. Thus the impact of laboratory errors and delays to the patient safety is significant, and has drawn increasing attention from both the general public and the healthcare professionals. Nowadays, the laboratory error rate is still high and continuously results in serious or irreversible medical consequences. It is critical to develop an effective and efficient quality system to prevent and reduce the errors and delays, or at least detect and correct them before it is too late. This study focuses on the risk assessment of patient safety in the entire processes (i.e. pre-analytical, analytical and post-analytical phases) in a clinical laboratory: Core Molecular Biology Laboratory (Core BM) in Hospital Clínic de Barcelona, which was newly-built in January 2016. It is a prospective risk assessment that helps to evaluate and improve the designed processes before their full implementation, to ensure the laboratory quality as well as patient safety ultimately. According to ISO standards and guidelines, the processes of the Core BM were assessed using Failure Modes and Effects Analysis (FMEA), with the help of Fishbone Cause-Effect Diagram. 216 risks were identified, the majority of which were from pre-analytical and analytical phases. 21 risks were ranked as high or medium priority to be treated, which mainly focused on sample quality and manual procedures. Actions were proposed to relevant processes for implementation. This is the first study in Europe that applied FMEA in a hospital clinical laboratory in the TTP scope, i.e. pre-analytical, analytical and post-analytical phases of Core BM. It has laid the foundation of the risk management system in the laboratory, and allows the future improvement from both detailed steps and general scope.