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      Total evidence analysis elucidates the tangled systematic scenario within Fidicinini (Hemiptera: Auchenorrhyncha, Cicadidae)

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      Journal: Arthropod Systematics & Phylogeny
      Publisher: Pensoft Publishers

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          Abstract

          The Linnean, Wallacean, and Darwinian shortfalls are knowledge gaps about species taxonomy, distribution, and evolution, respectively. Fidicinini is a tribe of cicadas that suffers from these gaps. We assessed specimens of the tribe sharing similar male genital shape (uncus), but fitting the somatic morphology of either Dorisiana Metcalf, 1952 and Guyalna Boulard & Martinelli, 1996. We build a phylogenetic hypothesis by total evidence analysis and perform a character optimization of the uncus and timbal cover shapes, the last used as diagnostic for both genera. Dorisiana and Guyalna were recovered non-monophyletic. A new genus, Acanthoventris gen. nov., and ten new species are proposed: A. charrua Ruschel sp. nov., A. claudiae Ruschel sp. nov., A. faustopsaltrius Ruschel sp. nov., A. iara Ruschel sp. nov., A. igneus Ruschel sp. nov., A. olivarius Ruschel sp. nov., A. phoenix Ruschel sp. nov., A. rubemi Ruschel sp. nov., A. tumidus Ruschel sp. nov., and A. viridinotatus Ruschel sp. nov.; and three new combinations A. densusus (Boulard & Martinelli, 2011) comb. nov., A. drewseni (Stål, 1854) comb. nov., and A. jauffreti (Boulard & Martinelli, 2001) comb. nov. We provide illustrated identification keys, occurrence maps, and discuss the distribution of the species in the new genus.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          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: Bayesian phylogenetic inference under mixed models.

            Fredrik Ronquist, John P Huelsenbeck (2003)
            MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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              SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

              Gaurav Vaidya, David Lohman, Rudolf Meier (2011)
              We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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                Author and article information

                Contributors
                Tatiana Petersen Ruschel: (View ORCID Profile)
                Filipe Michels Bianchi: (View ORCID Profile)
                Luiz Alexandre Campos: (View ORCID Profile)
                Gervásio Silva Carvalho: (View ORCID Profile)
                Journal
                Title: Arthropod Systematics & Phylogeny
                Abbreviated Title: ASP
                Publisher: Pensoft Publishers
                ISSN (Electronic): 1864-8312
                ISSN (Print): 1863-7221
                Publication date Created: January 20 2023
                Publication date (Electronic): January 20 2023
                Volume: 81
                Pages: 35-77
                Article
                DOI: 10.3897/asp.81.e85755
                SO-VID: 421a5932-4911-409d-820c-bf9d5dc6dd40
                Copyright © © 2023
                License:

                http://creativecommons.org/licenses/by/4.0/

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