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      Molecular Systematics of the Firefly Genus Luciola (Coleoptera: Lampyridae: Luciolinae) with the Description of a New Species from Singapore

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          Abstract

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          Fireflies have a scattered distribution in Singapore but are not as uncommon as many would generally assume. A nationwide survey of fireflies in 2009 across Singapore documented 11 species, including “ Luciola sp. 2”, which is particularly noteworthy because the specimens were collected from a freshwater swamp forest in the central catchment area of Singapore and did not fit the descriptions of any known Luciola species. Ten years later, we revisited the same locality to collect new specimens and genetic material of Luciola sp. 2. Subsequently, the mitochondrial genome of that population was sequenced and specimens were subjected to rigorous morphological examinations. We then collated published mitogenomes and shorter mitochondrial markers from closely related taxa to infer a phylogeny for the subfamily Luciolinae. Our results reveal that Luciola sp. 2 is both genetically and morphologically distinct from other congeners and is thus described herein as a new species Luciola singapura sp. nov. This marks the first time since 1909 that a new species of luminous firefly has been discovered in Singapore, highlighting the need for continued biodiversity research, even in small, well-studied and highly developed countries such as Singapore that can still harbor undescribed biodiversity.

          Abstract

          The firefly genus Luciola sensu McDermott contains 282 species that are distributed across major parts of Asia, Europe, Africa, Australia, and the Pacific islands. Due to phenotypic similarities, species identification using external morphological characters can be unreliable for this group. Consequently, decades of piecemeal taxonomic treatments have resulted in numerous erroneous and contentious classifications. Furthermore, our understanding of the group’s evolutionary history is limited due to the lack of a robust phylogenetic framework that has also impeded efforts to stabilize its taxonomy. Here, we constructed molecular phylogenies of Luciola and its allies based on combined mitogenomes and Cytochrome c oxidase subunit 1 ( COX1) sequences including a newly sequenced mitogenome of an unidentified taxon from Singapore. Our results showed that this taxon represents a distinct and hitherto undescribed evolutionary lineage that forms a clade with L. filiformis from Japan and L. curtithorax from China. Additionally, the Singaporean lineage can be differentiated from other congeners through several external and internal diagnostic morphological characters, and is thus described herein as a new species. Our phylogeny also strongly supported the paraphyly of Luciola with regard to L. cruciata and L. owadai, which were inferred to be more closely related to the genus Aquatica as opposed to other members of Luciola sensu stricto. The genus Hotaria was inferred as a derived clade within Luciola (sister to L. italica), supporting its status as a subgenus of Luciola instead of a distinct genus. This is the first time since 1909 that a new species of luminous firefly has been discovered in Singapore, highlighting the need for continued biodiversity research, even in small, well-studied and highly developed countries, such as Singapore.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

              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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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Animals (Basel)
                Animals (Basel)
                animals
                Animals : an Open Access Journal from MDPI
                MDPI
                2076-2615
                04 March 2021
                March 2021
                : 11
                : 3
                : 687
                Affiliations
                [1 ]Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore
                [2 ]School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga 2678, Australia; lballantyne@ 123456csu.edu.au
                [3 ]Central Nature Reserve, National Parks Board, Singapore 573858, Singapore; chan_su_hooi@ 123456nparks.gov.sg
                [4 ]National Parks Board HQ (Raffles Building), Singapore Botanic Gardens, Singapore 259569, Singapore; tuanwah@ 123456gmail.com
                [5 ]Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; dbsdy@ 123456nus.edu.sg
                [6 ]Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong 52109, Malaysia; nada@ 123456frim.gov.my
                Author notes
                [* ]Correspondence: wfawan@ 123456gmail.com (W.F.A.J.); cko@ 123456nus.edu.sg (K.O.C.)
                Author information
                https://orcid.org/0000-0002-2995-8429
                https://orcid.org/0000-0002-1030-6308
                https://orcid.org/0000-0001-6270-0983
                Article
                animals-11-00687
                10.3390/ani11030687
                7998795
                a1f779a8-8141-493e-be1e-d353268bc6f5
                © 2021 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
                : 27 January 2021
                : 26 February 2021
                Categories
                Article

                hotaria,luciola cruciata,luciola owadai,nee soon swamp forest,taxonomy,phylogenetics,conservation

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