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      Two new xylophile cytheroid ostracods (Crustacea) from Kuril-Kamchatka Trench, with remarks on the systematics and phylogeny of the family Keysercytheridae, Limnocytheridae, and Paradoxostomatidae

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      Arthropod Systematics & Phylogeny
      Pensoft Publishers

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          Abstract

          Abstract Keysercythere reticulata sp. nov. and Redekea abyssalis sp. nov., collected from the wood fall submerged in the Kuril-Kamchatka Trench (Northwestern Pacific), are only the second records of the naturally occurring, wood-associated ostracod fauna from a depth of over 5000 m. At the same time, K. reticulata is the second and R. abyssalis is the third representative of their respective genera. While Keysercythere Karanovic and Brandão, 2015 species are free-living, deep-sea taxa, all Redekea de Vos, 1953 live symbiotically on the body surface of wood-boring isopods, Limnoria spp. Since R. abyssalis is the only genus representative found in the deep sea, we hypothesize that its ancestor colonized this ecosystem as a result of the symbiotic relationship. Newly collected material enabled us to update molecular phylogeny of Cythreoidea based on 18S rRNA gene sequences, especially to clarify the current systematics of the families Keysercytheridae, Limnocytheridae, and Paradoxostomatidae. The resulting phylogenetic tree supports a close relationship between Keysercythere and Redekea and a distant relationship between two Limnocytheridae lineages, Timiriaseviinae and Limnocytherinae. Consequently, we propose a transfer of Redekea from Paradoxostomatidae to Keysercytheridae, and erecting of the two limnocytherid subfamilies onto the family level. The phylogenetic analysis also implies a close relationship between the nominal Limnocytherinae genus and Keysercythere+Redekea clade, albeit with a low posterior probability, requiring further studies to clarify this.

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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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              Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

              S Altschul (1997)
              The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                Arthropod Systematics & Phylogeny
                ASP
                Pensoft Publishers
                1864-8312
                1863-7221
                June 09 2021
                June 09 2021
                : 79
                : 171-188
                Article
                10.3897/asp.79.e62282
                02c9b786-9401-4d96-86cf-8c04c3d6ef88
                © 2021

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

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