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      Evolution and phylogeny of glass-sponge-associated zoantharians, with a description of two new genera and three new species

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          Abstract

          Hexactinellid sponges are important members of deep-sea benthic ecosystems because they provide available hard substrate habitats for filter-feeding invertebrates. However, symbioses between hexactinellid sponges and their symbionts are poorly known. Zoantharians associated with hexactinellid sponges have been reported widely from deep-sea marine ecosystems, either on the bodies or stalks of hexactinellid sponges. Despite these records, there has been a lack of research on their diversity and phylogenetic relationships. In this study, 20 specimens associated with amphidiscophoran and hexasterophoran sponges were collected from the waters of Australia and Japan in the Pacific, and from Curaçao in the southern Caribbean, and these were examined in addition to museum specimens. Based on molecular phylogenetic analyses and morphological observations, we formally describe two new genera and three new species of Zoantharia and report several previously described species. The results suggest at least two independent origins for the symbioses between hexactinellid sponges and zoantharians. Our results demonstrate that the diversity of hexactinellid sponge-associated zoantharians is much higher than has been previously thought. The new taxa described in this work further reconfirm that the deep-sea harbours high levels of undescribed zoantharian diversity.

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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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            Is Open Access

            Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

            Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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              MrBayes 3: Bayesian phylogenetic inference under mixed models.

              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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                Author and article information

                Contributors
                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                January 01 2022
                January 01 2022
                September 29 2021
                January 01 2022
                January 01 2022
                September 29 2021
                : 194
                : 1
                : 323-347
                Affiliations
                [1 ]Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
                [2 ]Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
                [3 ]Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
                [4 ]Okinawa Institute of Science and Technology, Evolution, Cell Biology and Symbiosis Unit, Onna, Okinawa, Japan
                [5 ]Taxonomy, Systematics, and Geodiversity Group, Naturalis Biodiversity Center, RA Leiden, The Netherlands
                [6 ]Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700 CC Groningen, The Netherlands
                [7 ]Queensland Museum, South Brisbane, 4101, Brisbane, Queensland, Australia
                [8 ]Griffith Institute of Drug Discovery, Griffith University, Brisbane, Queensland, Australia
                [9 ]School of Biological Sciences, University of Queensland, St Lucia, 4072, Queensland, Australia
                [10 ]Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Motobu, Okinawa, Japan
                [11 ]Okinawa Churaumi Aquarium, Okinawa Churashima Foundation, 424 Ishikawa, Motobu, Okinawa, Japan
                [12 ]Department of Biochemistry, Genetics and Immunology (School of Biology), University of Vigo, Vigo, Spain
                Article
                10.1093/zoolinnean/zlab068
                8ab7ce13-8bbc-433a-a211-300f259c48be
                © 2021

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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