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      Three new species of subterranean amphipods (Pseudocrangonyctidae: Pseudocrangonyx) from limestone caves in South Korea

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      PeerJ
      PeerJ Inc.
      Crangonyctoidea, Identification key, Molecular analyses, Morphological variations, Stygobitic fauna

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          Abstract

          Pseudocrangonyx Akatsuka & Komai, 1922 is the most diverse group of subterranean amphipods in the groundwater communities of Far East Asia. In Korea, the diversity of the group has been underestimated due to the records of morphological variants of Pseudocrangonyx asiaticus Uéno, 1934. To estimate the species diversity, we analyzed the morphological characteristics and conducted molecular analyses of specimens collected from Korean caves that we treated as morphological variants of P. asiaticus. We described three new subterranean pseudocrangonyctid amphipod species, P. deureunensis sp. nov., P. kwangcheonseonensis sp. nov. , and P. hwanseonensis sp. nov., from the groundwater of limestone caves in South Korea. Additionally, we determined sequences of the nuclear large subunit ribosomal RNA and the mitochondrial cytochrome c oxidase subunit I gene of the new species for molecular analyses. Molecular phylogenetic analyses revealed that the three new species formed a monophylum together with P. joolaei Lee et al., 2020 and P. wonkimi Lee, Tomikawa & Min, 2020, which are species that are endemic to Korean caves.

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          Most cited references31

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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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              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

                Contributors
                Journal
                PeerJ
                PeerJ
                peerj
                peerj
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                27 January 2021
                2021
                : 9
                : e10786
                Affiliations
                [-1] Department of Biological Sciences, Inha University , Incheon, South Korea
                Article
                10786
                10.7717/peerj.10786
                7847200
                454f089e-0a41-4326-b39c-f11d90aa0932
                ©2021 Lee and Min

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 23 October 2020
                : 24 December 2020
                Funding
                Funded by: Nakdonggang National Institute of Biological Resources (NNIBR)
                Funded by: Ministry of Environment (MOE) of the Republic of Korea
                Award ID: NNIBR111-1301
                Award ID: NNIBR201901203
                Funded by: Inha University
                This study work was supported by a grant from the Nakdonggang National Institute of Biological Resources (NNIBR) funded by the Ministry of Environment (MOE) of the Republic of Korea (NNIBR 111-1301, NNIBR201901203), and by Inha University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
                Categories
                Biodiversity
                Molecular Biology
                Taxonomy
                Zoology
                Freshwater Biology

                crangonyctoidea,identification key,molecular analyses,morphological variations,stygobitic fauna

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