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      Investigations into the ancestry of the Grape-eye Seabass (Hemilutjanus macrophthalmos) reveal novel limits and relationships for the Acropomatiformes (Teleostei: Percomorpha)

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          Abstract

          Abstract For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.

          Translated abstract

          Resumen Durante más de 175 años el Serranido ojo de uva (Hemilutjanus macrophthalmos), un pez parecido a la lubina común, se conoce de las zonas costeras del Pacífico Oriental. Al día de hoy la posición filogenética de esta especie se desconoce. Un estudio preliminar de Hemilutjanus basado en caracteres osteológicos sugirió que esta especie puede tener afinidades con el orden Acropomatiformes. Para investigar la posición filogenética de Hemilutjanus y los límites y relaciones dentro del orden Acropomatiformes realizamos análisis filogenéticos utilizando datos de secuencias Sanger y de UCEs. Demostramos que Hemilutjanus es un malakichthyid y nuestros resultados recobran Polyprionidae como una familia polifilética corroboran así estudios anteriores. En consecuencia, diagnosticamos y describimos una nueva familia de peces, Stereolepididae, que incluye ambas especies del genero Stereolepis. Con esta revisión, ahora el orden Acropomatiformes se compone de las familias: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, nueva familia; Symphysanodontidae; Synagropidae; y Schuettea. Finalmente, utilizando nuestra hipótesis filogenética, demostramos que bioluminiscencia ha evolucionado varias veces dentro de los miembros de Acropomatiformes y tambien demostramos múltiples transiciones entre aguas someras y zonas profundas del océano dentro de este grupo.

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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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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                ni
                Neotropical Ichthyology
                Neotrop. ichthyol.
                Sociedade Brasileira de Ictiologia (Maringá, PR, Brazil )
                1679-6225
                1982-0224
                2022
                : 20
                : 3
                : e210160
                Affiliations
                [6] Washington DC orgnameNational Museum of Natural History orgdiv1Department of Vertebrate Zoology USA girardmg@ 123456si.edu
                [7] Saint Cloud Minnesota orgnameSaint Cloud State University orgdiv1Department of Biological Sciences United States mpdavis@ 123456stcloudstate.edu
                [1] Lawrence Kansas orgnameUniversity of Kansas orgdiv1Department of Ecology and Evolutionary Biology and Biodiversity Institute United States leosmith@ 123456ku.edu
                [4] Chicago IL orgnameField Museum of Natural History USA cmcmahan@ 123456fieldmuseum.org
                [3] Quito orgnameFacultad de Biología Universidad Michoacana de San Nicolas de Hidalgo> orgdiv1Laboratorio de Biología cuatica Ecuador goodeido@ 123456yahoo.com.mx
                [2] Denver Colorado orgnameRegis University orgdiv1Department of Biology United States mghedott@ 123456regis.edu
                [5] Islas Galápagos, orgnameDirección del Parque Nacional Galápagos Ecuador eespinoza@ 123456galapagos.gob.ec
                Article
                S1679-62252022000300203 S1679-6225(22)02000300203
                10.1590/1982-0224-2021-0160
                11622f21-b8ae-4868-8424-0b63a9008082

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                : 16 May 2022
                : 18 November 2021
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 161, Pages: 0
                Product

                SciELO Brazil

                Categories
                Original Article

                Aguas profundas,Bioluminiscencia,Filogenia,Taxonomia,UCE,Bioluminescence,Deep sea,Phylogeny,Taxonomy

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