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      Complete mitochondrial genome of Plecialongiforceps Duda, 1933 (Diptera, Bibionidae) and its implications for a phylogeny of the family Bibionidae

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          Abstract

          Over the past decade, the prevalence of mass outbreaks involving non-native insects has sparked concerns about their potential negative impact on human inhabited areas and local environments. Plecia longiforceps Duda, 1933 ( Diptera , Bibionidae ) was recently recognized as an invasive pest in South Korea, causing public nuisance through mass outbreaks in the Seoul Metropolitan Area during early summer. In this study, we present the first complete mitochondrial genome of Plecia longiforceps , generated from the PacBio HiFi long-read sequencing data. Notably, the length of the circular genome is found to be larger than any annotated reference sequences of mitochondrial genomes for the infraorder Bibionomorpha , which is attributable to an unusually long A+T rich control region. We conducted a phylogenetic analysis of Bibionomorpha , focusing specifically on the family Bibionidae , using nearly all available mitochondrial genome data to elucidate relationships among genera within Bibionidae . Our phylogeny of Bibionomorpha recovered a strong monophyly of the family Bibionidae and its three subfamilies: Bibioninae ( Bibio + Dilophus ), Hesperininae ( Hesperinus + Penthetria ), and Pleciinae ( Plecia ), corroborating the recently proposed taxonomic classification system of Bibionidae . Furthermore, we discuss evolutionary trends within Bibionidae based on our well-supported higher relationships of the superfamily Bibionoidea .

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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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            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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              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.

                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2024
                12 September 2024
                : 1212
                : 1-15
                Affiliations
                [1 ] School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
                [2 ] Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Republic of Korea
                [3 ] Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
                Author notes
                Corresponding author: Seunggwan Shin ( sk83@ 123456snu.ac.kr)

                Academic editor: Netta Dorchin

                Author information
                https://orcid.org/0000-0002-8065-6696
                https://orcid.org/0000-0003-2758-8943
                https://orcid.org/0000-0002-4258-8661
                Article
                117845
                10.3897/zookeys.1212.117845
                11413505
                39309169
                e3605064-93cc-418a-9689-2b1e909b0b19
                Seunghun Jung, Sangil Kim, Seunggwan Shin

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 31 December 2023
                : 23 July 2024
                Funding
                This study is supported by the Creative-Pioneering Researchers Program through Seoul National University. The work is also funded by grants from the National Research Foundation of Korea (NRF) under the Ministry of Education, Science, and Technology (MEST) (No. 2019R1A6A1A10073437) and the Ministry of Science and ICT (MSIT) (No. 2021R1C1C1003452). Additional support is provided by the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (No. NIBR202311101, NIBR202333201).
                Categories
                Research Article
                Bibionomorpha
                Phylogeny

                Animal science & Zoology
                bibionidae,bibionomorpha,invasive species,long-read sequencing,mitogenome,phylogenetic analysis

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