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      Description of a new genus and species for a common and widespread Amazonian satyrine butterfly (Lepidoptera: Nymphalidae: Satyrinae: Satyrini)

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          Abstract

          We here propose a new monotypic butterfly genus Scriptor Nakahara & Espeland, n. gen. to accommodate a new species, S. sphenophorus Lamas & Nakahara, n. sp., described and named herein. Scriptor sphenophorus n. gen. and n. sp.is a relatively common and widespread butterfly species which is recovered as a member of the so-called “ Splendeuptychia clade” in the nymphalid subtribe Euptychiina, based on our molecular phylogenetic analysis using a maximum likelihood approach. Nevertheless, its sister group is not confidently resolved in any analysis, supporting a relatively distant relationship to any described genus as well as our decision to establish a new monotypic genus. We further discuss the proposed taxonomy in the light of frequent criticism of the description of monotypic taxa, as well as emphasize the importance of incorporating multiple evidence when describing new genera, illustrated by reference to several recent generic descriptions in this subtribe.

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          ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

          Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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            IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

            Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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              New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

              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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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                peerj
                peerj
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                4 December 2020
                2020
                : 8
                : e10324
                Affiliations
                [1 ]McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida , Gainesville, FL, United States of America
                [2 ]Department of Entomology and Nematology, University of Florida , Gainesville, FL, United States of America
                [3 ]Museo de Historia Natural, Universidad Nacional Mayor de San Marcos , Lima, Peru
                [4 ]Arthropoda Department, Zoological Research Museum Alexander Koenig , Bonn, Germany
                Article
                10324
                10.7717/peerj.10324
                7720727
                48ad87a1-9e43-433a-b71f-162b939ee731
                ©2020 Nakahara et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 23 July 2020
                : 19 October 2020
                Funding
                Funded by: Leverhulme Trust
                Funded by: Darwin Initiative
                Funded by: FLMNH Museum Associates
                Funded by: National Geographic Society
                Award ID: Research and Exploration Grant #5751-96
                Funded by: National Science Foundation
                Award ID: #0103746
                Award ID: #0639977
                Award ID: #0639861
                Award ID: #0847582
                Award ID: #1256742
                Funded by: McGuire Center Publication Fund
                Funded by: University of Florida’s Entomology and Nematology Department
                This study was funded by the Leverhulme Trust, the Darwin Initiative, the FLMNH Museum Associates, the National Geographic Society (Research and Exploration Grant # 5751-96), the National Science Foundation (#0103746, #0639977, #0639861, #0847582, #1256742), and by the McGuire Center Publication Fund. Shinichi Nakahara received financial support from the University of Florida’s Entomology and Nematology Department. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biodiversity
                Entomology
                Molecular Biology
                Taxonomy
                Zoology

                euptychiina,monotypic taxa,systematics,taxonomy
                euptychiina, monotypic taxa, systematics, taxonomy

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