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      Discovery of a new scale worm (Annelida: Polynoidae) with presumed deep-sea affinities from an anchialine cave in the Balearic Islands (western Mediterranean)

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      Zoological Journal of the Linnean Society
      Oxford University Press (OUP)

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          Abstract

          A remarkable new genus and species of scale worm (Annelida: Polynoidae) was found on the bottom sediments of an anchialine cave on the island of Mallorca (Balearic Islands, western Mediterranean). Specimens reach up to 2 cm long, lack eyes and body pigmentation except for a few scattered minute speckles and show enlarged parapodia and sensorial appendages. A red brain is visible through the translucent tegument. Morphological features resemble those of Eulagiscinae, currently comprising eight species in three genera. Phylogenetic analyses of mitochondrial and nuclear DNA sequences are not conclusive on the position of the new taxon but affinity to Eulagiscinae is not ruled out, particularly when taxa with missing data or non-homologous insertion sites are excluded from the analyses. Pollentia perezi gen. & sp. nov. is characterized by a unique set of morphological features: 13 pairs of dorsal elytra; a single type of notochaetae (stout, with spinous rows and pointed tip); and two types of neurochaetae (superior flattened, spinous with tridentate tip; inferior shorter and thinner, lanceolate and pectinate). Some characteristics, such as the long parapodial appendages and swimming habits, are shared with other cave scale worms. However, the new taxon is not closely related to the other two known cave-dwelling polynoids.

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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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            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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              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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                Author and article information

                Contributors
                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                September 01 2022
                August 26 2022
                July 30 2022
                September 01 2022
                August 26 2022
                July 30 2022
                : 196
                : 1
                : 479-502
                Article
                10.1093/zoolinnean/zlac046
                9e45625c-62c2-400e-b3a0-544f0819c617
                © 2022

                https://academic.oup.com/pages/standard-publication-reuse-rights

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