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      Primula dongchuanensis ( Primulaceae ), a new species from northern Yunnan, China

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          Abstract

          Abstract

          Primula dongchuanensis Z.K.Wu & Yuan Huang, a new species of Primulaceae from Dongchuan of northern Yunnan, China, is described and illustrated. Both morphological and molecular evidence support P. dongchuanensis as a member of the sect. Proliferae . It is similar to P. aurantiaca W.W.Smith & Forrest, but is distinguished by having unique raceme inflorescences. Its distribution, phenology and conservation status are also provided.

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          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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            New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

            Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)
            PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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              UFBoot2: Improving the Ultrafast Bootstrap Approximation

              Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler … (2017)
              Abstract The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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                Author and article information

                Contributors
                Yuan Huang
                Journal
                Journal ID (nlm-ta): PhytoKeys
                Journal ID (iso-abbrev): PhytoKeys
                Journal ID (publisher-id): 3
                Journal ID (index): urn:lsid:arphahub.com:pub:F7FCE9108E78573F9C777788555F8AAD
                Title: PhytoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-2011
                ISSN (Electronic): 1314-2003
                Publication date Collection: 2019
                Publication date (Electronic): 29 August 2019
                Volume: 130
                Pages: 171-181
                Affiliations
                [1 ] Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China Guizhou University of Traditional Chinese Medicine Guiyang China
                [2 ] Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, China Nanjing Institute of Environmental Sciences Nanjing China
                [3 ] Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
                [4 ] Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, School of Life Sciences, Yunnan Normal University, Kunming, 650001, China Yunnan Normal University Kunming China
                Author notes
                Corresponding author: Yuan Huang ( huangyuan@ 123456mail.kib.ac.cn )

                Academic editor: Ting Zhang

                Article
                Accession ID: PMC6728386 Pmcid ID: PMC6728386 Pmc-uid ID: 6728386 Publisher ID: 35047
                DOI: 10.3897/phytokeys.130.35047
                PMC ID: 6728386
                PubMed ID: 31534405
                SO-VID: 2be93f1e-1e72-4d3e-89b0-50768a69eaa5
                License:

                This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

                History
                Date received : 01 April 2019
                Date accepted : 28 June 2019
                Categories
                Subject: Research Article
                Subject: Primulaceae
                Subject: Biodiversity & Conservation
                Subject: Asia
                Subject: China

                Keywords: new species, Primula dongchuanensis , Primulaceae ,Yunnan,China
                Data availability:
                Keywords: new species, Primula dongchuanensis , Primulaceae , Yunnan, China

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