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      Higher-Level Phylogeny and Reclassification of Lampyridae (Coleoptera: Elateroidea)

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          Abstract

          Fireflies (Lampyridae Rafinesque) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ features. Due in part to their morphological diversity, the classification within the Lampyridae has long been in flux. Here we use an anchored hybrid enrichment approach to reconstruct the most extensive molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and use this phylogeny to evaluate the higher-level classification of the group. None of the currently recognized subfamilies were recovered as monophyletic with high support. We propose several classification changes supported by both phylogenetic and morphological evidence: 1) Pollaclasis Newman, Vestini McDermott (incl. Vesta Laporte, Dodacles Olivier, Dryptelytra Laporte, and Ledocas Olivier), Photoctus McDermott, and Araucariocladus Silveira & Mermudes are transferred to Lampyridae incertae sedis, 2) Psilocladinae Mcdermott, 1964status novum is reestablished for the genus Psilocladus Blanchard, 3) Lamprohizini Kazantsev, 2010 is elevated to Lamprohizinae Kazantsev, 2010status novum and Phausis LeConte is transferred to Lamprohizinae, 4) Memoan Silveira and Mermudes is transferred to Amydetinae Olivier, and 5) Scissicauda McDermott is transferred to Lampyrinae Rafinesque.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            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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              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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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                Insect Systematics and Diversity
                Oxford University Press (OUP)
                2399-3421
                November 2019
                November 01 2019
                November 2019
                November 01 2019
                December 17 2019
                : 3
                : 6
                Affiliations
                [1 ]Department of Biology, LSB, Brigham Young University, Provo, UT
                [2 ]Department of Plant Biology, University of Georgia, Athens, GA
                [3 ]Department of Entomology & Nematology, University of Florida, Gainesville, FL
                [4 ]Department of Genetics, University of Georgia, Athens, GA
                [5 ]Department of Biology, Bucknell University, Lewisburg, PA
                [6 ]Max-Planck Junior Scientist Group on Evolutionary Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Jiaochang Donglu Kunming, Yunnan
                [7 ]Department of Scientific Computing, Florida State University, Tallahassee, FL
                [8 ]Department of Biological Science, Florida State University, Tallahassee, FL
                [9 ]Monte L. Bean Museum of Natural History, Brigham Young University, Provo, UT
                Article
                10.1093/isd/ixz024
                32ef7ab1-1ffc-4df5-beba-2202a9a50186
                © 2019

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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