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      Click Beetle Mitogenomics with the Definition of a New Subfamily Hapatesinae from Australasia (Coleoptera: Elateridae)

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      Insects

      MDPI

      taxonomy, mitochondrial genomes, phylogeny, Gondwana, Australian region, new subfamily, new status

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          Abstract

          Simple Summary

          The classification of click beetles is revisited with newly sequenced mitochondrial genomes of eight species belonging to seven different subfamilies. The genus Hapatesus Candèze, 1863, is herein excluded from Dentrometrinae and designated as a type genus of Hapatesinae, a new subfamily. Phylogenetic analyses suggest that Eudicronychinae is a terminal lineage in Elaterinae. Consequently, we propose Eudicronychini, a new status. The deep mtDNA-based split between Elaterinae and the clade of other click beetle subfamilies agrees with the results of phylogenomic analyses and mitochondrial genomes provide a sufficient signal for inference of shallow splits.

          Abstract

          Elateridae is a taxon with very unstable classification and a number of conflicting phylogenetic hypotheses have been based on morphology and molecular data. We assembled eight complete mitogenomes for seven elaterid subfamilies and merged these taxa with an additional 22 elaterids and an outgroup. The structure of the newly produced mitogenomes showed a very similar arrangement with regard to all earlier published mitogenomes for the Elateridae. The maximum likelihood and Bayesian analyses indicated that Hapatesus Candèze, 1863, is a sister of Parablacinae and Pityobiinae. Therefore, Hapatesinae, a new subfamily, is proposed for the Australian genera Hapatesus (21 spp.) and Toorongus Neboiss, 1957 (4 spp.). Parablacinae, Pityobiinae, and Hapatesinae have a putative Gondwanan origin as the constituent genera are known from the Australian region (9 genera) and Neotropical region ( Tibionema Solier, 1851), and only Pityobius LeConte, 1853, occurs in the Nearctic region. Another putative Gondwanan lineage, the Afrotropical Morostomatinae, forms either a serial paraphylum with the clade of Parablacinae, Pityobiinae, and Hapatesinae or is rooted in a more terminal position, but always as an independent lineage. An Eudicronychinae lineage was either recovered as a sister to Melanotini or as a deep split inside Elaterinae and we herein transfer the group to Elaterinae as Eudicronychini, a new status. The mitochondrial genomes provide a sufficient signal for the placement of most lineages, but the deep bipartitions need to be compared with phylogenomic analyses.

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          Most cited references 72

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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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            MITOS: improved de novo metazoan mitochondrial genome annotation.

            About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
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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

                Journal
                Insects
                Insects
                insects
                Insects
                MDPI
                2075-4450
                29 December 2020
                January 2021
                : 12
                : 1
                Affiliations
                Laboratory of Biodiversity and Molecular Evolution, CATRIN-CRH, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic; dominik.kusy@ 123456upol.cz (D.K.); michal.motyka@ 123456upol.cz (M.M.)
                Author notes
                [* ]Correspondence: ladislav.bocak@ 123456upol.cz
                [†]

                These authors contributed equally to this work.

                Article
                insects-12-00017
                10.3390/insects12010017
                7859858
                33383651
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

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