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      Describing the hidden species diversity of Chaetozone (Annelida, Cirratulidae) in the Norwegian Sea using morphological and molecular diagnostics

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          Abstract

          Using molecular markers and species delimitation analyses, a high diversity of bi-tentaculate Cirratulidae was discovered from the North-East Atlantic. Five new species are described: Chaetozone pseudosetosa sp. nov., Chaetozone quinta sp. nov., Chaetozone barentsensis sp. nov., Chaetozone monteverdii sp. nov., and Chaetozone chambersae sp. nov. Several morphogroups are also described, even though the presence of cryptic diversity prevented naming of individual species. For each species presented, a molecular diagnostic is given from the universal barcode COI and, when available, the D1–D2 domains of the 28S rRNA. This increases the number of species in Chaetozone in northern European waters from ten to at least 17 species, the exact number of species remaining uncertain as taxonomic issues with older names remain unresolved.

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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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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

              Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2021
                21 May 2021
                : 1039
                : 139-176
                Affiliations
                [1 ] University of the Balearic Island, Department of Biology, Ctra. Valldemossa km 7.5, Balearic Islands, Spain University of the Balearic Islands Palma Spain
                [2 ] Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway Norwegian University of Science and Technology, NTNU University Museum Trondheim Norway
                Author notes
                Corresponding author: Maël Grosse ( maelgrosse@ 123456gmail.com )

                Academic editor: C. Glasby

                Author information
                https://orcid.org/0000-0002-0977-1376
                https://orcid.org/0000-0002-5063-7961
                https://orcid.org/0000-0002-5188-7305
                Article
                61098
                10.3897/zookeys.1039.61098
                8163715
                7c8b342c-3e6a-44d2-9683-828215713ea7
                Maël Grosse, María Capa, Torkild Bakken

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 24 November 2020
                : 19 March 2021
                Funding
                Funded by: Ministerio de Economía, Industria y Competitividad, Gobierno de España 501100010198 http://doi.org/10.13039/501100010198
                Categories
                Research Article
                Animalia
                Annelida
                Cirratulidae
                Invertebrata
                Polychaeta
                Terebellida
                Molecular Systematics
                Nomenclature
                Systematics
                Taxonomy
                Atlantic Ocean
                Europe
                Northern Europe
                Oceans

                Animal science & Zoology
                continental shelf,cryptic species,integrative taxonomy,new species,north-east atlantic,norway,polychaetes

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