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      Multilocus phylogeny and species delimitation suggest synonymies of two Lucanus Scopoli, 1763 (Coleoptera, Lucanidae) species names

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          Abstract

          Phylogenetic relationsships of four nominal Lucanus Scopoli, 1763 species, L. swinhoei Parry, 1874, L. continentalis Zilioli, 1998, L. liuyei Huang & Chen, 2010, and L. wuyishanensis Schenk, 1999, are assessed based on mitochondrial (16S rDNA, COI) and nuclear (28S rDNA, Wingless) genes. The genetic distance is 0.0072 between L. swinhoei and L. continentalis , and 0.0094 between L. wuyishanensis and L. liuyei . Three species-delimitation approaches (ABGD, PTP, and GMYC) consistently showed L. swinhoei + L. continentalis and L. wuyishanensis + L. liuyei as two MOTUs. A new synonymy, L. liuyei = L. wuyishanensis , is proposed. Synonymy of L. swinhoei over L. continentalis is confirmed.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)
            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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              W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

              Jana Trifinopoulos, Lam-Tung Nguyen, Arndt von Haeseler … (2016)
              This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary models including mixture and partition models. W-IQ-TREE performs fast model selection, partition scheme finding, efficient tree reconstruction, ultrafast bootstrapping, branch tests, and tree topology tests. All computations are conducted on a dedicated computer cluster and the users receive the results via URL or email. W-IQ-TREE is available at http://iqtree.cibiv.univie.ac.at. It is free and open to all users and there is no login requirement.
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                Author and article information

                Contributors
                Xia Wan
                Journal
                Journal ID (nlm-ta): Zookeys
                Journal ID (iso-abbrev): Zookeys
                Journal ID (publisher-id): 2
                Journal ID (index): urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                Title: ZooKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1313-2989
                ISSN (Electronic): 1313-2970
                Publication date Collection: 2022
                Publication date (Electronic): 14 December 2022
                Volume: 1135
                Pages: 139-155
                Affiliations
                [1 ] Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
                [2 ] Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, 111 Jiulong Rd., Hefei, 230601, China
                [3 ] Department of Entomology, University of Wisconsin Madison, WI 53706, USA
                Author notes
                Corresponding author: Xia Wan (wanxia@ahu.edu.cn)

                Academic editor: Andrey Frolov

                Author information
                https://orcid.org/0000-0003-3113-7811
                Article
                Publisher ID: 89257
                DOI: 10.3897/zookeys.1135.89257
                PMC ID: 9836572
                PubMed ID: 36761796
                SO-VID: fa0bf6bc-64d0-4ea0-82d1-c897620eeec5
                Copyright statement: Li Yang Zhou, Zhi Hong Zhan, Xue Li Zhu, Xia Wan
                License:

                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
                Date received : 20 June 2022
                Date accepted : 23 November 2022
                Product
                Self URI (zoobank): http://zoobank.org/1E8F80E7-EA62-4071-A64F-4DC412181E68
                Funding
                National Natural Science Foundation of China (No. 31872276; 31572311).
                Categories
                Subject: Research Article
                Subject: Lucanidae
                Subject: Scarabaeoidea
                Subject: Molecular Systematics
                Subject: Taxonomy
                Subject: Cenozoic
                Subject: Asia

                ScienceOpen disciplines: Animal science & Zoology
                Keywords: genetic distance,lucanidae,morphology,new synonymy,phylogenetic analysis,species delimitation
                Data availability:
                ScienceOpen disciplines: Animal science & Zoology
                Keywords: genetic distance, lucanidae, morphology, new synonymy, phylogenetic analysis, species delimitation

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