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      Phylogenetic position of the ‘extinct’ Fijian coconut moth, Levuana iridescens (Lepidoptera: Zygaenidae)

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      1 , * , 2 , 3
      PLoS ONE
      Public Library of Science

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          Abstract

          Levuana iridescens Bethune-Baker, 1906, a day-flying moth purported to be endemic to the Fijian Island of Viti Levu and a former pest of its coconut palm trees, was last observed in 1956 and has been officially declared extinct by IUCN since 1996. The controversial classical biological control method that resulted in the (presumed) demise of this moth has given this species an iconic status in biological control studies. We investigated the sister-group relationships and phylogenetic placement of this moth using NGS-obtained ancient DNA sequences from museum specimens of L. iridescens collected in the 1920s, combined with 31 morphological characters used in earlier studies and 2 new characters. Our findings show that Levuana is most closely related to the Australian genus Myrtartona. The significance of these findings is discussed.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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            MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

            Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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              Assessing risks of releasing exotic biological control agents of arthropod pests.

              More than 5000 introductions of about 2000 species of exotic arthropod agents for control of arthropod pests in 196 countries or islands during the past 120 years rarely have resulted in negative environmental effects. Yet, risks of environmental effects caused by releases of exotics are of growing concern. Twenty countries have implemented regulations for release of biological control agents. Soon, the International Standard for Phytosanitary Measures (ISPM3) will become the standard for all biological control introductions worldwide, but this standard does not provide methods by which to assess environmental risks. This review summarizes documented nontarget effects and discusses the development and application of comprehensive and quick-scan environmental risk assessment methods.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Funding acquisitionRole: InvestigationRole: ResourcesRole: Writing – review & editing
                Role: Funding acquisitionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                5 December 2019
                2019
                : 14
                : 12
                : e0225590
                Affiliations
                [1 ] Independent Researcher, Ottawa, Ontario Canada
                [2 ] Naturwissenschaftliche Sammlungen, Sammlungs- und Forschungszentrum der Tiroler Landesmuseen, Krajnc-Straße 1, Hall, Austria
                [3 ] V. I. Vernadsky Crimean Federal University, Simferopol, Crimea
                Museum National d'Histoire Naturelle, FRANCE
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-9064-8959
                Article
                PONE-D-19-11660
                10.1371/journal.pone.0225590
                6894762
                31805075
                9253c4bc-578c-470d-9cf8-2bde0bc931ef
                © 2019 Nazari et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 29 April 2019
                : 7 November 2019
                Page count
                Figures: 3, Tables: 2, Pages: 13
                Funding
                This research was supported through funding to the Canadian Barcode of Life Network from Genome Canada (through the Ontario Genomics Institute), NSERC and other sponsors listed at www.bolnet.ca. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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                Biology and Life Sciences
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                Custom metadata
                dx.doi.org/10.5883/DS-LEVUANA

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