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      Deeper diversity exploration: New Typhlotanaidae (Crustacea: Tanaidacea) from the Kuril-Kamchatka Trench area

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      Frontiers in Marine Science
      Frontiers Media SA

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          Abstract

          Typhlotanaidae Sieg, 1984, is one of the most diverse Tanaidacea families from deep-sea waters. Its diversity is underestimated, and evolutionary relationships within the family remain mostly unknown. Deep-sea typhlotanaids collected from 23 sites across the Kuril-Kamchatka Trench and nearby waters were studied using an integrative taxonomy approach, combining morphological and genetic data (i.e., the mitochondrial subunit I of the cytochrome oxidase (COI) and the 18S rDNA nuclear gene). One new species of Typhlamia and two new species belonging to two new genera are described, significantly increasing the known diversity of typhlotanaids from the NW Pacific. The molecular phylogeny obtained, despite being preliminary results, was congruent with morphological data and supports the monophyly of different groups such as the ‘short-bodied’ forms (represented by Ty. cornutus and Ty. eximius) or the ‘collar’ forms (e.g., Ty. variabilis and Torquella). Molecular data confirm the non-monophyly of Typhlotanais species. Finally, the new typhlotanaid taxa seem to have distinct bathymetric distribution and ecological requirements, but further data on environmental factors and species abundances are still needed.

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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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              Basic local alignment search tool.

              A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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                Author and article information

                Journal
                Frontiers in Marine Science
                Front. Mar. Sci.
                Frontiers Media SA
                2296-7745
                September 2 2022
                September 2 2022
                : 9
                Article
                10.3389/fmars.2022.927181
                4d1dbb45-6630-42db-9b89-497a8a634e90
                © 2022

                Free to read

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

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