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

      research-article
      , , *
      Insects
      MDPI
      taxonomy, mitochondrial genomes, phylogeny, Gondwana, Australian region, new subfamily, new status

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          Abstract

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          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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          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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            fastp: an ultra-fast all-in-one FASTQ preprocessor

            Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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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
                : 17
                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.

                Author information
                https://orcid.org/0000-0001-8893-8981
                https://orcid.org/0000-0002-5167-3948
                https://orcid.org/0000-0001-6382-8006
                Article
                insects-12-00017
                10.3390/insects12010017
                7859858
                33383651
                c4b7480c-7561-4263-9cd6-1dcd79f3761b
                © 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/).

                History
                : 08 December 2020
                : 23 December 2020
                Categories
                Article

                taxonomy,mitochondrial genomes,phylogeny,gondwana,australian region,new subfamily,new status

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