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      • Record: found
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      A new species of Munida Leach, 1820 (Crustacea: Decapoda: Anomura: Munididae) from seamounts of the Nazca-Desventuradas Marine Park

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          Abstract

          Munida diritas sp. nov. is described for the seamounts near Desventuradas Islands, in the intersection of the Salas & Gómez and Nazca Ridges, Chile. Specimens of the new species were collected in the summit (∼200 m depth) of one seamount and observed by ROV at two nearby ones. This species is characterized by the presence of distinct carinae on the thoracic sternites 6 and 7. Furthermore, it is not related with any species from the continental shelf nor the slope of America, while it is closely related to species of Munida from French Polynesia and the West-Pacific Ocean (i.e., M. ommata, M. psylla and M. rufiantennulata). In situ observations indicate that the species lives among the tentacles of ceriantarid anemones and preys on small crustaceans. The discovery of this new species adds to the knowledge of the highly endemic benthic fauna of seamounts of the newly created Nazca-Desventuradas Marine Park, emphasizing the relevance of this area for marine conservation.

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

          R. C. Edgar (2004)
          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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            Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

            Matthew Kearse, Richard Moir, Amy Wilson … (2012)
            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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              MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

              K Katoh (2002)
              A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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                Author and article information

                Contributors
                María de los Ángeles Gallardo Salamanca
                Journal
                Journal ID (nlm-ta): PeerJ
                Journal ID (iso-abbrev): PeerJ
                Journal ID (publisher-id): peerj
                Journal ID (pmc): peerj
                Title: PeerJ
                Publisher: PeerJ Inc. (San Diego, USA )
                ISSN (Electronic): 2167-8359
                Publication date (Electronic): 5 January 2021
                Publication date Collection: 2021
                Volume: 9
                Electronic Location Identifier: e10531
                Affiliations
                [1 ]Sala de Colecciones Biológicas, Facultad de Ciencias del Mar, Universidad Católica del Norte , Coquimbo, Chile
                [2 ]Departamento de Biología Marina & Núcleo Milenio Ecología y Manejo Sustentable de Islas Oceánicas, Universidad Católica del Norte , Larrondo 1281, Coquimbo, Chile
                [3 ]Centre d’Estudis Avançats de Blanes (CEAB-CSIC) , Blanes, Spain
                [4 ]Programa de Magister en Ciencias del Mar Mención Recursos Costeros, Facultad de ciencias del Mar, Universidad Católica del Norte , Coquimbo, Chile
                Article
                Publisher ID: 10531
                DOI: 10.7717/peerj.10531
                PMC ID: 7792524
                PubMed ID: 33505787
                SO-VID: 95c2bfff-897d-4368-904e-d2397a572705
                Copyright © ©2021 Gallardo Salamanca et al.
                License:

                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
                Date received : 28 August 2020
                Date accepted : 19 November 2020
                Funding
                Funded by: CONA
                Award ID: C22 16-09
                Funded by: FONDECYT
                Award ID: 1181153
                Funded by: FONDEQUIP EQM
                Award ID: 150109
                Funded by: ANID-Millennium Science Initiative Program-ESMOI
                Funded by: Beca Magister Nacional CONICYT # 22190560
                Funded by: Beca Postdoctorado Universidad Católica del Norte No 003
                This work was supported by grants (CONA C22 16-09, FONDECYT 1181153, FONDEQUIP EQM 150109) and ANID-Millennium Science Initiative Program-ESMOI. Beca Magister Nacional CONICYT # 22190560 (now ANID) to Jan M. Tapia Guerra, Beca Postdoctorado Universidad Católica del Norte No 003 to María de los Ángeles Gallardo. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Biodiversity
                Subject: Conservation Biology
                Subject: Marine Biology
                Subject: Taxonomy
                Subject: Zoology

                Keywords: nazca ridges,deep-sea,pacific ocean,indo-pacific fauna,salas & gómez ridges
                Data availability:
                Keywords: nazca ridges, deep-sea, pacific ocean, indo-pacific fauna, salas & gómez ridges

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